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AcqKnowledge

4 Software Guide

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For Life Science Research Applications
Data Acquisition and Analysis with BIOPAC MP Systems



Reference Manual for
AcqKnowledge

4.3.1 Software & MP150/MP36R or BioHarness and B-Alert Hardware/Firmware


on Windows

8, 7 or Vista, or Mac OS

X 10.5-10.8









42 Aero Camino, Goleta, CA 93117
Tel (805) 685-0066 | Fax (805) 685-0067
info@biopac.com | www.biopac.com


2 AcqKnowledge 4 Software Guide

TABLE OF CONTENTS
PREFACE TO ACQKNOWLEDGE SOFTWARE GUIDE.................................................. 13
Welcome ................................................................................................................................................................. 13
Supported Platforms................................................................................................................................................ 13
Whats new for AcqKnowledge 4.3.1 ..................................................................................................................... 13
User Support System............................................................................................................................................... 17
Where do I find help?.............................................................................................................................................. 18
PART A GETTING STARTED....................................................................................... 21
Chapter 1 MP Systems Overview...........................................................................................................................21
MP36R support ....................................................................................................................................................... 22
MP System Requirements....................................................................................................................................... 22
Spotlight Importer for Graph Files.......................................................................................................................... 23
Automator Integration and Scripting Support ......................................................................................................... 24
MP System Features................................................................................................................................................ 25
Application Features ............................................................................................................................................... 28
MP System (MP150 or MP36R) Application Notes ............................................................................................... 29
Chapter 2 AcqKnowledge Overview.......................................................................................................................30
Launching the AcqKnowledge software ................................................................................................................. 32
Setting up channels ................................................................................................................................................. 34
Setting up acquisitions ............................................................................................................................................ 35
Starting an acquisition............................................................................................................................................. 35
Stopping an Acquisition.......................................................................................................................................... 36
Display modes......................................................................................................................................................... 37
Data Views.............................................................................................................................................................. 43
Analysis .................................................................................................................................................................. 44
Selecting a waveform.............................................................................................................................................. 46
Show/Hide Channel ................................................................................................................................................ 47
Zoom....................................................................................................................................................................... 47
Select an area .......................................................................................................................................................... 47
Keyboard data selection.......................................................................................................................................... 47
Transform data........................................................................................................................................................ 48
Measurements ......................................................................................................................................................... 48
Events (Markers)..................................................................................................................................................... 49
Grids........................................................................................................................................................................ 49
Horizontal Split View............................................................................................................................................. 49
Autoscroll Horizontal Axis Controls....................................................................................................................... 50
Journals ................................................................................................................................................................... 51
Saving data.............................................................................................................................................................. 51
Format change warnings ............................................................................................................................................51
Data Snapshot Embedded Archive ................................................................................................................. 52
Print......................................................................................................................................................................... 53
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Table of Contents 3
Chapter 3 User Interface & Context Menu Features ...........................................................................................54
Toolbars.............................................................................................................................................................................54
Toolbar.....................................................................................................................................................................55
Hardware Toolbar ....................................................................................................................................................56
Cursor Toolbar.........................................................................................................................................................56
Selection palette.......................................................................................................................................................60
Start/Stop toolbar .....................................................................................................................................................60
Channel Number Toolbar ........................................................................................................................................60
Events toolbar ..........................................................................................................................................................60
Focus Area Toolbar..................................................................................................................................................60
Measurements toolbar..............................................................................................................................................61
Custom toolbars for transformations and analysis ...................................................................................................61
Toolbar position retention and changes ...................................................................................................................61
Axis Controls ...........................................................................................................................................................62
Enable cursor tools during acquisitions ...................................................................................................................62
Button Transparency................................................................................................................................................62
Customizable Chart Track Dividers.........................................................................................................................62
Plotting Background Colors.....................................................................................................................................63
Spectrum Analyzer Palette.......................................................................................................................................63
Keyboard shortcuts ..................................................................................................................................................63
Mouse Controls........................................................................................................................................................67
Mouse Scrollwheel Support .....................................................................................................................................67
Transformation history.............................................................................................................................................68
Cancelling Transformations & Transformation Progress Bar..................................................................................68
Typed event label drawing improvements ...............................................................................................................68
Choose MP150 Help Button ....................................................................................................................................69
Tooltips ..............................................................................................................................................................................69
Channel label and units length and tooltips .............................................................................................................69
Graph window tooltip improvements ......................................................................................................................69
Menu item tooltips ...................................................................................................................................................69
Chapter 4 Editing and Analysis Features..............................................................................................................70
Scroll bars ................................................................................................................................................................70
Scaling .....................................................................................................................................................................71
Horizontal axis...........................................................................................................................................................71
Vertical (Amplitude) axis ..........................................................................................................................................72
Adaptive Scaling......................................................................................................................................................73
Show Textual Value Display ...................................................................................................................................73
Grid Details..............................................................................................................................................................75
Grid Options ..............................................................................................................................................................78
Journal Details .........................................................................................................................................................80
Journal Contextual Menu.........................................................................................................................................80
Rich Journals .............................................................................................................................................................81
Journal Toolbar Buttons.............................................................................................................................................81
Journal Numerical Table Tools..................................................................................................................................82
Example of Sum, Mean or Standard..........................................................................................................................83
Example of Evaluate Expression ...............................................................................................................................84
Adding a hyperlink to the Journal..............................................................................................................................84
Select a waveform / channel ......................................................................................................................................85
Channel Labels ........................................................................................................................................................85
Show/Hide Channel .................................................................................................................................................86
Focus Areas..............................................................................................................................................................86
Creating Focus Areas...............................................................................................................................................86
Measurements ..........................................................................................................................................................88
Measurement Display ................................................................................................................................................89
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Measurement Area.....................................................................................................................................................89
Measurements and Measurement Presets...................................................................................................................91
Measurement Validation............................................................................................................................................91
Measurement Info / Parameters .................................................................................................................................91
Measurement Interpolation ........................................................................................................................................92
Exporting measurements............................................................................................................................................92
PART BACQUISITION FUNCTIONS: THE MP MENU................................................ 103
Acquisitions .......................................................................................................................................................... 104
Chapter 5 Set Up Channels...................................................................................................................................105
Set Up ChannelsThe Basics........................................................................................................................................105
Module-based analog channel setup ..................................................................................................................... 105
View by Channels ................................................................................................................................................. 107
Set Up ChannelsAdvanced.........................................................................................................................................110
Analog channels.......................................................................................................................................................110
Increased Channel Count Support (AcqKnowledge 4.3 and above) ........................................................................111
Analog channels MP36R .........................................................................................................................................112
Offset .......................................................................................................................................................................112
Fixed Hardware Filters MP36R...............................................................................................................................112
Adjustable Hardware Filters MP36R.......................................................................................................................113
MP36R Advanced Preset Settings ...........................................................................................................................114
Calculation channels ................................................................................................................................................117
Metachannel.............................................................................................................................................................118
Chapter 6 Calculation Channel Presets................................................................................................................121
Integrate Calculation................................................................................................................................................122
Smoothing Calculation.............................................................................................................................................127
Difference Calculation.............................................................................................................................................128
Rate Calculation.......................................................................................................................................................129
Signal Parameters Tab .............................................................................................................................................130
Output Tab ...............................................................................................................................................................130
Function Calculation................................................................................................................................................133
Filter Calculation .....................................................................................................................................................134
Expression................................................................................................................................................................136
Delay Calculation.....................................................................................................................................................143
Fourier Linear Combiners: FLC, WFLC, CWFLC Calculations .............................................................................148
Basic FLC................................................................................................................................................................148
Weighted-Frequency FLC........................................................................................................................................148
Coupled WFLC/FLC................................................................................................................................................148
Adaptive Filtering Calculation.................................................................................................................................149
Comb Band Stop Filter Calculation .........................................................................................................................149
Metachannel.............................................................................................................................................................149
Rescale Calculation..................................................................................................................................................150
Chapter 7 Set Up Acquisition..............................................................................................................................151
Set Up AcquisitionThe Basics .......................................................................................................................... 151
Multiple Hardware...................................................................................................................................................155
Averaging.............................................................................................................................................................. 157
Overview..................................................................................................................................................................157
Averaging Setup.......................................................................................................................................................158
Advanced AveragingP300 ...................................................................................................................................160
Repeating .................................................................................................................................................................161
Starting an acquisition........................................................................................................................................... 163
Stopping an Acquisition........................................................................................................................................ 163
Rewind.................................................................................................................................................................. 163
Saving acquisition data ......................................................................................................................................... 164
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Table of Contents 5
Electrode Checker..................................................................................................................................................164
Chapter 8 Set Up Triggering.................................................................................................................................165
Digital Triggers......................................................................................................................................................165
Analog Triggers .....................................................................................................................................................166
Chapter 9 Set Up Stimulator ................................................................................................................................168
Analog Output for MP150 Users ...........................................................................................................................172
Dual Stimulation....................................................................................................................................................173
Square waves .........................................................................................................................................................174
Tone Stimuli ..........................................................................................................................................................175
Ramp Waves..........................................................................................................................................................175
Arbitrary Waveform...............................................................................................................................................176
Chapter 10 Output Control .....................................................................................................................................178
CH to Output..........................................................................................................................................................179
CH# to Output Output Control...............................................................................................................................180
MP36R Input > Output Scaling .............................................................................................................................181
Digital Outputs Control..........................................................................................................................................182
Pulses Output Control ............................................................................................................................................183
Stimulator BSLSTM Output Control ..................................................................................................................183
Stimulator Low Voltage Output Control.............................................................................................................183
Pulse Sequence Output Control .............................................................................................................................185
Sound Sequence Output Control............................................................................................................................187
Output Control Panel Descriptions ........................................................................................................................190
Usage Guidelines & Setup Summary for BSLSTM Output Control .....................................................................200
Chapter 11 Set Up Event Hotkeys..........................................................................................................................202
Events (Markers)....................................................................................................................................................202
Event (Marker) Overview........................................................................................................................................202
Event Toolbar ..........................................................................................................................................................203
Event Tooltips..........................................................................................................................................................203
Event Preferences ....................................................................................................................................................204
Event Hotkey Setup .................................................................................................................................................205
Create/Toggle Focus Area Action............................................................................................................................206
Event Palette ............................................................................................................................................................207
Event Type Options .................................................................................................................................................211
Event Measurements................................................................................................................................................214
Printing Events.........................................................................................................................................................216
Event Selection ........................................................................................................................................................216
Events and Graph Selections ...................................................................................................................................216
Events and Waveform Editing.................................................................................................................................217
Constructing Graph Selections from Events............................................................................................................217
Event Plotting and Variable Sampling Rate.............................................................................................................217
Chapter 12 Other MP menu Commands...............................................................................................................218
Show Input Values.................................................................................................................................................218
Manual Control ......................................................................................................................................................219
Set Up Linked Acquisitions ...................................................................................................................................220
Limitations on Linked Acquisitions synchronization methods..............................................................................222
Manage Hardware Connections.............................................................................................................................222
MP150 Info............................................................................................................................................................223
Update Firmware ...................................................................................................................................................223
Segment Labels......................................................................................................................................................223
Sound Feedback.....................................................................................................................................................224
Gauge.....................................................................................................................................................................225
Gauge Preferences ...................................................................................................................................................225
Segment Timer Stopwatch option ........................................................................................................................228
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MP36R support ..................................................................................................................................................... 230
Autoplot ................................................................................................................................................................ 230
Scroll ..................................................................................................................................................................... 230
Warn on Overwrite................................................................................................................................................ 230
Organize Channel Presets ..................................................................................................................................... 231
PART CANALYSIS FUNCTIONS................................................................................. 232
Toolbars ...................................................................................................................................................................232
Shortcuts ..................................................................................................................................................................232
Chapter 13 File Menu Commands ..........................................................................................................................233
New....................................................................................................................................................................... 233
Graph Window.........................................................................................................................................................233
New > Graph-specific Journal .................................................................................................................................233
New > Independent Journal .....................................................................................................................................233
New > Data View.....................................................................................................................................................233
New > Batch Acquisition.........................................................................................................................................233
Batch Errors .............................................................................................................................................................234
Open...................................................................................................................................................................... 236
Open Recent.......................................................................................................................................................... 241
Open for Playback................................................................................................................................................. 241
SMI BeGaze Import .............................................................................................................................................. 242
Close ..................................................................................................................................................................... 243
Save....................................................................................................................................................................... 244
Save As ................................................................................................................................................................. 244
Save Selection As ................................................................................................................................................. 250
Save Journal Text As ............................................................................................................................................ 251
File Format prompts.................................................................................................................................................251
Send Email Attachment ........................................................................................................................................ 252
Page setup ............................................................................................................................................................. 252
Print....................................................................................................................................................................... 252
Quit ....................................................................................................................................................................... 253
Chapter 14 Edit menu commands...........................................................................................................................254
Undo / Cant undo................................................................................................................................................. 255
Cut......................................................................................................................................................................... 256
Copy...................................................................................................................................................................... 256
Paste...................................................................................................................................................................... 256
Clear...................................................................................................................................................................... 257
Clear all................................................................................................................................................................. 257
Select All............................................................................................................................................................... 257
Insert waveform.................................................................................................................................................... 257
Duplicate waveform.............................................................................................................................................. 258
Remove waveform................................................................................................................................................ 258
Remove last appended segment ............................................................................................................................ 258
Create Data Snapshot ............................................................................................................................................ 258
Merge Graphs........................................................................................................................................................ 259
Clipboard .............................................................................................................................................................. 260
Journal................................................................................................................................................................... 261
Chapter 15 Transform menu commands................................................................................................................264
Recently Used Transformations............................................................................................................................ 265
Digital Filters ........................................................................................................................................................ 265
FIR Filters ................................................................................................................................................................268
Digital filter dialog...................................................................................................................................................268
IIR Filters.................................................................................................................................................................270
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Table of Contents 7
Adaptive Filtering....................................................................................................................................................271
Comb Band Stop Filter ............................................................................................................................................271
Fourier Linear Combiners......................................................................................................................................274
Basic FLC................................................................................................................................................................274
Weighted-Frequency FLC .......................................................................................................................................274
Math Functions ......................................................................................................................................................276
Template Functions................................................................................................................................................278
Set Template ............................................................................................................................................................278
Remove mean ..........................................................................................................................................................279
Template algorithms ................................................................................................................................................280
Adaptive Template Matching ..................................................................................................................................282
Integral ...................................................................................................................................................................284
Derivative ..............................................................................................................................................................284
Integrate .................................................................................................................................................................286
Output Reset ............................................................................................................................................................286
Smoothing..............................................................................................................................................................289
Difference ..............................................................................................................................................................290
Resample................................................................................................................................................................291
Resample Graph.......................................................................................................................................................291
Resample Waveform................................................................................................................................................291
Expression..............................................................................................................................................................292
Delay......................................................................................................................................................................292
Rescale...................................................................................................................................................................293
Waveform math .....................................................................................................................................................293
Chapter 16 Analysis Menu Commands ..................................................................................................................295
Histogram ..............................................................................................................................................................295
Autoregressive Modeling.......................................................................................................................................296
Nonlinear Modeling...............................................................................................................................................297
Power Spectral Density..........................................................................................................................................299
AR Time-Frequency Analysis ...............................................................................................................................299
FFT Fast Fourier Transformation ..........................................................................................................................300
Inverse FFT..............................................................................................................................................................303
DWT Discrete Wavelet Transformation................................................................................................................305
Inverse DWT..........................................................................................................................................................305
Principal Component Analysis...............................................................................................................................305
Inverse PCA.............................................................................................................................................................305
Independent Component Analysis .........................................................................................................................306
Inverse ICA..............................................................................................................................................................306
Find Cycle (Peak Detector)....................................................................................................................................307
Cycles/Peaks tab ......................................................................................................................................................307
Find Next Cycle.....................................................................................................................................................308
Find All Cycles in Graph.......................................................................................................................................308
Find in Selected Area.............................................................................................................................................308
Find All Cycles in Focus Areas .............................................................................................................................308
Find First Cycle .....................................................................................................................................................308
Preview..................................................................................................................................................................308
Find Cycle definitions............................................................................................................................................308
Selection tab.............................................................................................................................................................311
Output tab ................................................................................................................................................................312
Output Measurements ..............................................................................................................................................312
Output: AveragingOffline....................................................................................................................................312
Output 3D Surface ...................................................................................................................................................313
Output Events ..........................................................................................................................................................314
Event definition........................................................................................................................................................314
Event Location Table...............................................................................................................................................315
Output Focus Area...................................................................................................................................................316
Output: Clustering....................................................................................................................................................317
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Algorithm Overview................................................................................................................................................318
Clustering Settings ...................................................................................................................................................319
Number of clusters...................................................................................................................................................319
Locate Centers .........................................................................................................................................................319
Manually ..................................................................................................................................................................319
By Learning .............................................................................................................................................................319
Training Set Definition ............................................................................................................................................320
Remove Outliers ......................................................................................................................................................320
Clustering Criteria....................................................................................................................................................321
Clustering Output.....................................................................................................................................................321
Find Rate............................................................................................................................................................... 324
Modes of Operation .............................................................................................................................................. 324
Additional Find Rate Dialog Settings, Output Tab..................................................................................................329
Specialized Analysis ............................................................................................................................................. 330
Chapter 17 Specialized Analysis..............................................................................................................................331
Detect and Classify Heartbeats ............................................................................................................................. 334
Locate Human ECG Complex Boundaries ........................................................................................................... 334
Locate Animal ECG Complex Boundaries ........................................................................................................... 334
Heart Rate Variability ........................................................................................................................................... 335
RR intervals .......................................................................................................................................................... 337
Frequency Bands................................................................................................................................................... 338
PSD Options.......................................................................................................................................................... 338
Improvements to PSD Options (AcqKnowledge 4.3 and higher).......................................................................... 340
Gastric Wave Analysis.......................................................................................................................................... 341
Gastric Wave Coupling......................................................................................................................................... 342
Chaos Analysis...................................................................................................................................................... 342
Detrended Fluctuation Analysis...............................................................................................................................342
Optimal Embedding Dimension...............................................................................................................................343
Optimal Time Delay.................................................................................................................................................343
Plot Attractor............................................................................................................................................................343
Correlation Coefficient ......................................................................................................................................... 344
Electrodermal Activity.......................................................................................................................................... 344
Derive Phasic EDA from Tonic ...............................................................................................................................345
Event-related EDA Analysis....................................................................................................................................345
Sorting Options ........................................................................................................................................................348
Locate SCRs.............................................................................................................................................................350
EDA Measurements .................................................................................................................................................351
Electroencephalography........................................................................................................................................ 353
Compute Approximate Entropy...............................................................................................................................353
Delta Power Analysis...............................................................................................................................................353
Derive Alpha RMS ..................................................................................................................................................354
Derive EEG Frequency Bands .................................................................................................................................354
EEG Frequency Analysis .........................................................................................................................................355
Remove EOG Artifacts ............................................................................................................................................356
Preferences...........................................................................................................................................................357
Electromyography................................................................................................................................................. 358
Derive Average Rectified EMG...............................................................................................................................358
Derive Integrated EMG............................................................................................................................................358
Derive Root Mean Square EMG..............................................................................................................................359
EMG Frequency & Power Analysis.........................................................................................................................359
Locate Muscle Activation ........................................................................................................................................359
Preferences...........................................................................................................................................................360
Ensemble Average ................................................................................................................................................ 361
Epoch Analysis ..................................................................................................................................................... 362
Focus Areas........................................................................................................................................................... 363
Hemodynamic Analysis ........................................................................................................................................ 363
ABP Classifier .........................................................................................................................................................364
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Table of Contents 9
Arterial Blood Pressure............................................................................................................................................364
ECG Interval Extraction ..........................................................................................................................................365
HRV Poincare Plot...................................................................................................................................................365
Left Ventricular Blood Pressure ..............................................................................................................................366
LVP Classifier..........................................................................................................................................................367
Monophasic Action Potential...................................................................................................................................368
MAP Classifier ........................................................................................................................................................369
Respiratory Sinus Arrhythmia .................................................................................................................................369
Preferences...............................................................................................................................................................370
Impedance Cardiography Analysis ........................................................................................................................371
Body Surface Area...................................................................................................................................................371
dZ/dt Derive from Raw Z ........................................................................................................................................371
dZ/dt Classifier ........................................................................................................................................................371
ICG Analysis ...........................................................................................................................................................374
Ideal Body Weight ...................................................................................................................................................377
PEP Pre-ejection Period...........................................................................................................................................377
dZ/dt Remove Motion Artifacts...............................................................................................................................378
VEPT .......................................................................................................................................................................378
Preferences...............................................................................................................................................................379
Magnetic Resonance Imaging................................................................................................................................380
Artifact Frequency Removal....................................................................................................................................380
Artifact Projection Removal ....................................................................................................................................382
Median Filter Artifact Removal...............................................................................................................................382
Signal Blanking........................................................................................................................................................383
Slew Rate Limiter ....................................................................................................................................................383
Neurophysiology....................................................................................................................................................384
Amplitude Histograms.............................................................................................................................................384
Average Action Potentials .......................................................................................................................................384
Classify Spikes.........................................................................................................................................................385
Dwell Time Histograms...........................................................................................................................................385
Find Overlapping Spike Episodes............................................................................................................................386
Generate Spike Trains..............................................................................................................................................386
Locate Spike Episodes .............................................................................................................................................386
Set Episode Width and Offset..................................................................................................................................387
Preferences...............................................................................................................................................................387
Noldus Format .......................................................................................................................................................389
Principal Component Denoising............................................................................................................................390
Remove Mean........................................................................................................................................................390
Remove Trend........................................................................................................................................................390
Respiration.............................................................................................................................................................391
Compliance and Resistance .....................................................................................................................................391
Penh Analysis ..........................................................................................................................................................393
Pulmonary Airflow..................................................................................................................................................394
Preferences...............................................................................................................................................................396
Spectral Subtraction...............................................................................................................................................396
Stim-Response .......................................................................................................................................................396
Digital Input to Stim Events ....................................................................................................................................397
Stim-Response Analysis ..........................................................................................................................................399
Waterfall Plot.........................................................................................................................................................399
Wavelet Denoising.................................................................................................................................................400
ECG Analysis Algorithm References ....................................................................................................................401
Chapter 18 Display menu commands .....................................................................................................................403
Tile Waveforms .....................................................................................................................................................404
Autoscale Waveforms............................................................................................................................................404
Autoscale Single Waveform..................................................................................................................................405
Overlap Waveforms...............................................................................................................................................406
Compare Waveforms .............................................................................................................................................406
Autoscale Horizontal .............................................................................................................................................407
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Zoom Back / Forward ........................................................................................................................................... 407
Reset Chart Display .............................................................................................................................................. 407
Reset Grid ............................................................................................................................................................. 408
Adjust Grid Spacing.............................................................................................................................................. 408
Set Wave Positions................................................................................................................................................ 408
Wave Color ........................................................................................................................................................... 409
Active Slice Color....................................................................................................................................................409
Horizontal Axis..................................................................................................................................................... 410
Show..................................................................................................................................................................... 411
Customize Toolbars .................................................................................................................................................414
Spectrum Analyzer Palette.......................................................................................................................................415
Channel Info.......................................................................................................................................................... 418
Preferences... ......................................................................................................................................................... 419
Measurements Preferences.......................................................................................................................................422
Waveforms Preferences ...........................................................................................................................................423
Event Summary Preferences ....................................................................................................................................423
Graph Preferences....................................................................................................................................................424
Journal Preferences ..................................................................................................................................................425
Hardware Preferences ..............................................................................................................................................425
Performance Preferences..........................................................................................................................................425
Networking Preferences...........................................................................................................................................425
Other Preferences.....................................................................................................................................................426
Window Preferences ................................................................................................................................................426
Focus Area Preferences............................................................................................................................................426
Scroll options ...........................................................................................................................................................427
Size window.......................................................................................................................................................... 427
Cursor Style .......................................................................................................................................................... 427
Create Data View.................................................................................................................................................. 427
Create Focus Area................................................................................................................................................. 427
Organize Data Snaphots........................................................................................................................................ 428
Show All Data Snaphots ....................................................................................................................................... 428
Load All Data Into Memory.................................................................................................................................. 428
Chapter 19 Program & OS Menus..........................................................................................................................429
AcqKnowledge menu............................................................................................................................................ 429
Window menu....................................................................................................................................................... 429
Bring All to Front.....................................................................................................................................................429
Help menu............................................................................................................................................................. 429
Chapter 20 Media Menu..........................................................................................................................................431
Synchronization Tip.............................................................................................................................................. 432
Media > Set Up..................................................................................................................................................... 433
Linked Media........................................................................................................................................................ 433
Media > Capture ................................................................................................................................................... 434
Playback Preview.................................................................................................................................................. 434
Media Playback Example...................................................................................................................................... 435
Chapter 21 Licensed Functionality: Network Data Transfer...............................................................................436
Data Connections .................................................................................................................................................. 437
Variable Sampling Rates....................................................................................................................................... 437
Transfer Types ...................................................................................................................................................... 437
Single Connection....................................................................................................................................................438
Multiple Connection ................................................................................................................................................438
XML-RPC................................................................................................................................................................439
Transport Protocol................................................................................................................................................. 439
TCP/IP .....................................................................................................................................................................439
UDP .........................................................................................................................................................................439
XML-RPC................................................................................................................................................................440
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Table of Contents 11
Real-time Delivery Guarantees..............................................................................................................................440
Data Formats..........................................................................................................................................................441
Default Data Connection Settings..........................................................................................................................441
Locating AcqKnowledge Servers...........................................................................................................................442
Control Connections ..............................................................................................................................................442
TCP Port ................................................................................................................................................................442
Control Procedure Calls.........................................................................................................................................443
Channel Index Parameter Structures........................................................................................................................443
Querying Acquisition Parameters ............................................................................................................................443
Data Connection Configuration Commands ............................................................................................................444
Reading Data During Acquisition............................................................................................................................448
Other Control Connection Commands.....................................................................................................................448
Chapter 22 Licensed Functionality: Vibromyography .........................................................................................450
Sampling Rate Restrictions......................................................................................................................................450
Transducer Setup .....................................................................................................................................................450
Post-analysis Selection Adjustment .........................................................................................................................451
Data Modification History Name.............................................................................................................................451
VMG Calculation Channel Preset............................................................................................................................451
VMG Sample Data Files..........................................................................................................................................452
Chapter 23 Licensed Functionality: Scripting.......................................................................................................453
Chapter 24 Licensed Functionality: Remote Monitoring .....................................................................................456
About Remote Monitoring.......................................................................................................................................456
Remote Monitoring in AcqKnowledge Networking Preferences ............................................................................456
Remote Monitoring Client .......................................................................................................................................457
Remote Monitoring Client Browser.........................................................................................................................457
Open Graphs Page ...................................................................................................................................................459
Configuration Settings Page ....................................................................................................................................459
Data Monitoring Page..............................................................................................................................................461
Controls in Visible Range (Change Range) dialog..................................................................................................462
Chapter 25 Licensed Functionality: B-Alert ..........................................................................................................463
Data Acquisition and Analysis with B-Alert......................................................................................................463
Acquisition Setup...................................................................................................................................................466
Channel Setup........................................................................................................................................................466
B-Alert-specific Hardware Menu Options .............................................................................................................467
Assign Definition File............................................................................................................................................469
Output to ABM File Format (AcqKnowledge 4.3 and higher only).......................................................................469
Chapter 26 Licensed Functionality: PV Loop Analysis ........................................................................................473
Chapter 27 Licensed Functionality: BioHarness Bluetooth..................................................................................479
Data Acquisition and Analysis with BIOPAC BioHarness................................................................................479
PART DAPPENDICES................................................................................................. 480
Appendix A - Frequently Asked Questions ..................................................................................................................480
Appendix B - Filter characteristics ...............................................................................................................................483
Filter types .............................................................................................................................................................483
Window Functions.................................................................................................................................................484
Appendix C - Hints for Working with Large Files ......................................................................................................486
Appendix D - Customizing Menu Functionality ..........................................................................................................487
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Appendix ELocking/Unlocking the MP150 for Network Operations ....................................................................488
Appendix FFirmware Upgrade .................................................................................................................................490
Firmware Rollback Switch.................................................................................................................................... 490
INDEX............................................................................................................................... 491

Preface to AcqKnowledge Software Guide
Welcome
Welcome to the AcqKnowledge Software Guide. The MP System (MP150 or MP36R) is a complete data
acquisition system that includes both hardware and software for the acquisition and analysis of life
science data. The MP System is used for data acquisition, analysis, storage, and retrieval.
AcqKnowledge software not only makes data collection easier, but also performs analyses more quickly
and easily than a chart recorder. Easily edit data, cut and paste sections of data, perform mathematical and
statistical transformations, and copy data to other applications (such as a drawing program or spreadsheet)
for reports and publication.
The MP System (MP150 or MP36R data acquisition unit) with AcqKnowledge 4 is compatible with
Windows

8, 7 or Vista OS or Mac OS X

10.5-10.8.
AcqKnowledge uses the familiar point-and-click interface common to all Windows

and Macintosh


applications. Complex tasks such as digital filtering or fast Fourier transformations are now as easy as
choosing a menu item or clicking your mouse.
This manual covers use of AcqKnowledge software with MP150/MP36/BioHarness/ B-Alert hardware
and details BIOPAC equipment available for a variety of applications. If a desired application is not
addressed, just visit the BIOPAC web site at www.biopac.com to download one of our many Application
Notes, or call to request a hard copy or talk to an Applications Specialist.

See also:
BIOPAC Installation Guidepacked with the software CD.
BIOPAC MP Hardware Guide.pdfavailable under the Help menu and installed to the User Support
folder. Provides details on MP System (MP150 or MP36R) modules, transducers, electrodes, etc., and
setup and calibration.
BIOPAC Catalogs

MP Research Catalog MRI catalog VR & Stimulus Catalog

Supported Platforms
AcqKnowledge 4.3 is supported on the following:
Operating Systems Comment Hardware
Windows 8, 7 or Vista32 MP150 UDP only
Windows 8, 7 or Vista64 32 bit mode only MP36R only
Windows XP Functional, limited testing BioHarness BT (Windows only)
Mac OS X 10.5-10.8 x86 B-Alert (Windows Orly)
Whats new for AcqKnowledge 4.3.1

14 AcqKnowledge 4 Software Guide
Visit the online support center at www.biopac.com
BONUS! AcqKnowledge includes a courtesy copy of our new Analysis package.
See the Analysis chapter for details.
Note New features for AcqKnowledge 4.0-4.3 apply to the English language version of the software only.
AcqKnowledge 3.9 software is translated for the following languages:
Chinese Simplified, Chinese Traditional, French, Italian, Japanese, and Spanish.
Contact BIOPAC to learn more AcqKnowledge 3.9 translations.

AcqKnowledge 4.3.1 is an interim bug-fix release. The following new features have been added since AcqKnowledge
4.3 was released.
- Horizontal split view allows viewing of two independent horizontal axis areas in same graph
- Journal hyperlinks and page setup tool
- High frame rate camera support
- MP150 communication improvements
- Labels for append events may be edited
- Preferences may be cleared by holding Shift key down while launching application
- File-specific output control presets for MP36R
- Files may be opened for Playback from the Startup Wizard
- New scripting commands for: changing output control preset, get acquisition sampling rate, change active output
control, callback for window activation, toggling output control, calibrate a channel of the graph
- Epoch Analysis option to start first interval at beginning of each focus area
- Support for MPMS200 and OXY300-MRI hardware
- New measurement validation sample data files with accompanying spreadsheets for verifying measurements
The following features have been added since AcqKnowledge 4.2 was released.
- Windows 8 supported
- OS X 10.8 supported in Mac version
- Linked acquisitions supporting multiple hardware
types
- Increased channel count support up to 15,000
channels
- Consolidated and multiple hardware support
- Improved compatibility for standard user account
presets/specialized analysis settings
- Bluetooth integration for BioHarness
- Scaled ECG boundary selection
- ICG Analysis improvements
- Pressure Volume Loop Analysis tools
- Find Cycle enhancements
- Rate Detector enhancements
- Graph Textual Value Display and Toolbar
- Original data restored after canceling
transfomations
- Focus Area feature
- Tabbed graph interface
- Noldus import/export
- SMI BeGaze data import
- Improved software controls for B-Alert

wireless
EEG system
- Higher resolution cameras supported in Media
Capture/Playback
- Media Capture/Playback now supports linking to
earlier-format AcqKnowledge 3.9/BSL 3.7 files
- Selection palette toolbar icon
- Linked selection option from the I-beam tool
- Measurement column selection
- Rate/Expression Presets
- Automated analysis changes to EEG - analyze
multiple channels in one go
- Additions to the ICG analysis
- Journal docking options
- New preference to pin dialog windows on top of
application
- New MP150 Modules for Heel/Toe Strike, Dyno
Clench Bulb and Goniometer setups

Preface 15
AcqKnowledge 4 Software Guide
The following features have been added since AcqKnowledge 4.1 was released.
BioNomadix wireless module support
Rich Journals
- Expressions in Journal
- Tables and Excel

functions
- Docked and independent Journal windows
MP36R universal built-in amp module support
- Pulse Sequence Output Control
- Sound Sequence Output Control
- Analog Channel scaling units adapt to gain
- Simplified Hardware Filtering options
Startup Wizard for launching application
Check for MP hardware function
Email graph image as attachment
Event enhancements
- Global Event label printing
- Customizable Event markers
- Customizable append segment labels
- Sequential Event labels
- Sorted Event summary
- Mark selection from Events
Measurement enhancements
- Single point measurements
- X/Y measurement label display
- Revised invalid measurement display
Media playback automatic segment advancement
User Interface Tools
- Most Recently Used options
- Preset menu separators
- Keyboard data selection enhancement
- Zoom out for Spectrum Analyzer
- Enable tools during acquisition (Preference)
- Cursor tools sub-menu
- Mouse scroll-wheel zoom support
Graph file display enhancements
- Select channel background
- Select line plot thickness
- Data Playback enhancements
- Start/End axis adjustment
- Horizontal Axis Hold Relative Position
- X/Y display crosshairs enhancement
- Customize default graph window position and size
- Default analog channel unit display preference
Grid enhancements
- Channel independent grid settings
- Grid presets
Gaussian Random Number Generator
Automated Analysis routine enhancements
- Poincare Plot Hemodynamic Analysis
- Locate Muscle Activation adjustable windowing
Advanced Averaging
Sound Feedback
Licensed functionality
- New Remote Monitoring bedside monitor
display
o View subject data remotely over a network
- New B-Alert X-10

Wireless EEG System


o EEG wireless headset integration
o Cognitive States Analysis
- BIOPAC Basic Scripting
o Script Editor Reset Defaults button

16 AcqKnowledge 4 Software Guide
Visit the online support center at www.biopac.com
Using this Manual
The AcqKnowledge Software Guide is divided into four parts:
Part A Getting Started
Please review Getting Started whether new to computer-based data acquisition systems or an old hand at
physiological monitoring. Use this section to become acquainted with how the system works and the most
frequently used features.
Part B Acquisition Functions
Explains data acquisition features and gives a detailed summary of different acquisition parameters. Provides
an in-depth description of the commands used to determine acquisition rate, acquisition duration, and
specialized functions such as triggering, averaging, and online calculation of different values.
Part C Analysis Functions
Details information on analysis features; covers the range of post-acquisition analysis functions and
transformations available with the MP System. Describes how to edit data, take measurements and perform
basic file management options (save, print, etc).
Part D Appendices
Answers frequently asked questions, offers hints for working with files, includes information on upgrading
from previous versions, provides technical information about the MP System and other information about the
AcqKnowledge software.

See also:
BIOPAC Installation Guide
This guide was included with the software CD. It contains full instructions for hardware and software
installation, and how to be up and running with the MP System in just a few minutes.

Hardware Guide
BIOPAC MP Hardware Guide.pdf is available under the Help menu. It gives practical examples of how the
MP data acquisition unit is used with different components for common types of data acquisition, and
includes sample results and applications for widely used test procedures. This guide provides instructions for
connecting external devices to the MP150 or MP36R, electrodes, transducers, amplifiers, etc.
Part A Getting Started 17
User Support System

User Support System files can be found in the following hard drive location; BIOPAC Systems, Inc/AcqKnowledge
3.x/User Support Systems in the Program Files or Applications folder.

AcqKnowledge Software Guide.pdf is the software support document

BIOPAC MP Hardware Guide.pdf is the hardware guide (with specifications)

The User Support files can also be opened directly from the CD.

The files are in PDF format, and can be read by Adobe Acrobat Reader.
- Adobe Acrobat Reader can be downloaded for free at www.adobe.com under the Adobe Acrobat Reader site.

The Samples folder in the BIOPAC program folder contains sample files and graph template Quick Start files for a
variety of applications. Quick Start templates establish the channel setup and acquisition parameters required for a
variety of applications.

- To open sample files, choose File > Open then Browse to the BIOPAC Samples folder.
- In addition to the standard sample files, measurement sample data files are provided. These files are
configured for specific measurement types and include spreadsheets providing external data necessary for
measurement verification. Each spreadsheet contains procedures and examples for the associated
measurement data file. These sample data files consist of Event Measurements.acq, Traditional.acq (standard
mathematical measurements included in AcqKnowledge,) Expression Sum_Calculate.acq and Correl
Coef.acq (Correlation Coefficient).
- To open a graph template Quick Start file, choose File > Open then Browse to the BIOPAC Samples folder
(be sure to select/enable the desired file type).

AcqKnowledge 4 Software Guide
18 AcqKnowledge 4 Software Guide
Where do I find help?
The Introductory sections are intended to provide enough information to get up and running with the MP System,
and become familiarized with some basic AcqKnowledge functions. There are far more features than described in the
first few pages, so here is a guide for how to continue using this manual.
Help menu
The online Help menu includes basic information about standard AcqKnowledge functions and links to the
tutorial, software guide and hardware guide for online searchable Help while running AcqKnowledge, plus
links to the BIOPAC web site.
You may also visit BIOPACs new Tutorial section at: www.biopac.com/videos.asp for instructional
screencasts of many analysis routines and software features.
Application Notes
The BIOPAC web site at http://www.biopac.com has more than 50 available Application Notes. Download
the desired Application Note or call to request a hard copy.
Acquiring data
For more specific information on different types of acquisitions, see Part BAcquisition Functions. It covers
basic acquisition parameters in detail, and describes some acquisition features (such as peak detection
techniques and online Calculation channels) not covered in the Getting Started section.
AcqKnowledge
Information about how to edit, display and transform data can be found in Part CAnalysis Functions. It
explains how to import and export data, how to save files, and other file management commands. This
section also explains how to use all of the post-acquisition features of the AcqKnowledge software.
Connecting input devices
To find out how specific modules connect to the MP data acquisition unit, turn to the BIOPAC MP
Hardware Guide PDF file. This section describes how to connect signal-conditioning modules to the MP
data acquisition unit and how to connect electrodes and transducers to the modules.
Working with large files
Many users need to perform high speed (i.e., fast sampling rates) or long duration acquisitions. These types
of acquisitions tend to generate large (several megabytes) data files that can be difficult to load, store, and
view. The MP System (MP150 or MP36R) can handle such acquisitionssee the Appendices for
information on how to optimize setup for these types of acquisitions.
Troubleshooting
Includes a list of the most frequently asked questions regarding the MP System (MP150 or MP36R). Check
this section (Appendix A) for commonly encountered problems and solutions.

Visit the online support center at www.biopac.com
Part A Getting Started 19


IMPORTANT SAFETY NOTICE
BIOPAC Systems, Inc. instrumentation is designed for educational and research-oriented life science
investigations. BIOPAC Systems, Inc. does not condone the use of its instruments for clinical medical applications.
Instruments, components, and accessories provided by BIOPAC Systems, Inc. are not intended for the diagnosis,
mitigation, treatment, cure, or prevention of disease.
The MP data acquisition unit is an electrically isolated data acquisition system, designed for biophysical
measurements.
Exercise extreme caution when applying electrodes and taking bioelectric measurements while using the MP
System (MP150 or MP36R) with other external equipment that also uses electrodes or transducers that may make
electrical contact with the Subject. Always assume that currents can flow between any electrodes or electrical
contact points.
Extreme caution is also required when performing general stimulation (electrical or otherwise) on a subject.
Stimulation currents should not be allowed to pass through the heart. Keep stimulation electrodes far from the heart
and located close together on the same side of the subjects body.
It is very important (in case of equipment failure) that significant currents are not allowed to pass through the heart.
If electrocautery or defibrillation equipment is used, it is recommended that all BIOPAC Systems, Inc.
instrumentation be disconnected from the Subject.


AcqKnowledge 4 Software Guide
20 AcqKnowledge 4 Software Guide
Human Anatomy & Physiology Society Position Statement on Animal Use
(Adopted July 28, 1995, Modified January 2001, Approved April 29, 2012)
It is the position of the Human Anatomy and Physiology Society (HAPS) that dissection and the manipulation of
animal tissues and organs are important elements in scientific investigation that introduce students to the excitement
and challenge of their future careers. HAPS supports the use of biological specimens as part of a program of study,
provided their use is in strict compliance with federal legislation and the guidelines of the National Institutes of
Health and the United States Department of Agriculture, and that such use fulfills clearly defined educational
objectives.
The mission of the Human Anatomy and Physiology Society (HAPS) is to promote excellence in the teaching of
anatomy and physiology. A fundamental tenet of science is the ordered process of inquiry requiring careful and
thoughtful observation by the investigator. As subdivisions of biology, both anatomy and physiology share a long
history of careful and detailed examination, exploration and critical inquiry into the structure and function of the
human and animal body.
Consistent with the origins and nature of scientific inquiry, HAPS endorses the use of animals as part of the
laboratory experiences in both human anatomy and human physiology.
Historically, an important tool of investigation in human and animal anatomy has been dissection. A complete
anatomy learning experience that includes dissection goes beyond naming structures and leads the student to
conclusions and insights about the nature and relatedness of living organisms that are not otherwise possible. To
succeed in their future careers, students must become thoroughly familiar with anatomical structures, their design
features and their relationships to one another. Dissection is based on observational and kinesthetic learning that
instills a recognition and appreciation for the three-dimensional structure of the animal body, the interconnections
between organs and organ systems, and the uniqueness of biological material. Dissection conveys the inherent
variability of living organisms not otherwise observable in simulations and models. Physiology experiments
involving humans and live animals provide an excellent opportunity to learn the basic elements specific to scientific
investigation and experimentation. It is here that students pose questions, propose hypotheses, develop technical
skills, collect data, analyze results and develop and improve critical thinking and problem solving skills
Since effective teaching requires a diversity of strategies and approaches, HAPS endorses the use of computer atlases
and simulations, modeling, and video programs to meet educational objectives and the needs of students. Science
educators choosing not to use animals or biological specimens should choose alternatives that are able to convey
equivalent anatomical and physiological intricacies to meet their educational objectives.
Science educators have in common a respect and reverence for the natural world and therefore have a responsibility
to share this with their students. They must communicate the importance of a serious approach to the study of
anatomy and physiology. HAPS also encourages educators to be responsive to student concerns regarding use of
animals and to provide students who object to animal use with alternative learning materials.
HAPS contends that science educators should retain responsibility for making decisions regarding the educational
uses of animals and other strategies and techniques for the betterment of their students learning. Furthermore, it
opposes any legislation or administrative policy that would erode the educators role in decision making or restrict
dissection and animal experimentation in biology.
Used with permission of:
The Human Anatomy & Physiology Society (HAPS)
251 S. L. White Blvd., P. O. Box 2945, LaGrange, GA 30241-2945
800-448-HAPS (4277) Fax: (706) 883-8215 www.hapsweb.org

Visit the online support center at www.biopac.com
Part A Getting Started 21
Part A Getting Started
Chapter 1 MP Systems Overview
Part A - Getting Started covers the basics of data acquisition and analysis with an MP System (MP150 or MP36R).
All of the material in this section is covered in more detail in subsequent sections (see Using this Manual, page 16 ).

BioHarness users should also see the BioHarness User Guide available under
the Help menu and installed to the User Support folder in the program folder.

Overview
The MP System (MP150 or MP36R) is a computer-based data acquisition system that performs many of the same
functions as a chart recorder or other data viewing device, but is superior to such devices in that it transcends the
physical limits commonly encountered (such as paper width or speed). Data collection generally involves taking
incoming signals (usually analog) and sending them to the computer, where they are (a) displayed on the screen and
(b) stored in the computers memory (or on the hard disk). These signals can then be stored for future examination,
much as a word processor program stores a document or a statistics program saves a data file. Graphical and
numerical representations of the data can also be produced for use with other programs.
Function MP150
Aggregate Sample Rate
Internal MP150 Buffer: 400 kHz
To Cpt. Memory or Disk: 300 kHz
Internal Buffer Size: 6 Mbytes
A/D Converter Signal/Noise Ratio: 86 dB typical
D/A Resolution: 16 bits
D/A Output rate: Independent of A/D rate
Communication to Computer: Ethernet (10 base T, UDP and DLC Type II)
The MP System utilizes the same hardware, excepting the computer interface. The software has the same look and
feel on computers running Windows

or Mac

OS X.
The system is referred to as MPWSW for Windows

or MPWS for Mac.


The MP System consists of several major components, including hardware and software. The AcqKnowledge
software included with the MP system allows full control over editing data, the way it appears on the screen, and
performs four general functions:
(a) Control the data acquisition process;
(b) Perform real-time calculations (such as digital filtering and rate detection);
(c) Perform post-acquisition transformations (such as FFTs and math functions);
(d) Handle file management commands (saving, printing, and the like).
The heart of the MP System) is the MP data acquisition unit, which converts incoming physiological data into digital
signals that can be processed and displayed on a computer interface. The MP150 data acquisition unit connects via
Ethernet, the MP36R connects via USB.
The MP150 System also includes a Universal Interface Module (UIM100C) for connecting external devices to the
MP150 data acquisition unit. Connect chart recorders, pre-amplified signals, and digital signals such as those from
triggers or event counters/recorders. The UIM100C connects to the front of the MP150 data acquisition unit via two
cables (Analog and Digital). As a rule, both cables should be connected. The connectors for each of the two cables
are different, so there is only one way the UIM100C can be connected to the MP150 data acquisition unit.
A wall transformer is included with the MP System (MP150 or MP36R) to convert AC mains power into DC power
suitable for system operation and safety.
AcqKnowledge 4 Software Guide
22 AcqKnowledge 4 Software Guide
MP36R support
The MP36R is a four-channel data acquisition unit designed to work with AcqKnowledge 4.1 and above for the
research market. AcqKnowledge support for the MP36R unit includes:
Standard data acquisition and data acquisition features (triggering, multiple channels, variable sampling rate,
input values)
Output control functionality for controlling stimulators, digital channel, and channel redirection to output.
Standard analog presets for all SS series transducers
Electrode Check support
Multiple-MP device support. Similar to multiple MP150 support, each graph may acquire from a maximum
of one unique MP device.
Control channel support for changing digital output lines based on calculation channel analysis

MP36R Notes The computer sleep mode should be disabledif the computer goes to sleep while AcqKnowledge 4
is running, communication with the MP36R may be lost and the application may freeze. To prevent
this from occurring, modify the computer settings to prevent the computer from going to sleep.
If sleep mode is enabled and causes the
application to freeze, force quit the application
and power cycle the MP unit to re-establish
communication.
During an unresponsive period, the Connect
Hardware dialog may display odd characters
in place of the MP serial number or the
computer, upon waking up, may generate a
Driver irql not less or equal error dialog.
AcqKnowledge software does not support MP36
units from the Biopac Student Lab product line (without the R designation).
Mac OS users: Connect the MP36R directly to the computer, do not connect MP36R via hub or
keyboard.
MP System Requirements
Suggested minimum system requirements are detailed below. Recommendations are included to optimize system
performance; more memory and a faster system will enhance MP System performance. If planning to acquire data
for more than a few hours and/or are sampling at more than 1,000 samples per second, see the Disk Space note.
Windows For AcqKnowledge 4.3
OS Requires Windows 8, 7 or Vista or Mac OS X 10.5-10.8
Port
MP150 Requires Ethernet (UDP), MP36R requires USB.
Note To use an MP150 with UDP communication on a network with a non-Windows DHCP server,
it is necessary to use firmware rev. 1.1.12 or greater in order for the MP150 unit to properly be
assigned an IP address. This is also true for any DHCP system with non-Windows operating
systems, such as Unix, Linux, Mac OS X, and other DHCP-aware devices.
Hard Disk
Requires 1 GB to store the software and online manuals; additional 1 GByte recommended for data
storage
RAM 1 GB recommended
Processor
PC: Pentium 4 or higher
Mac: Intel Core Duo or higher

Visit the online support center at www.biopac.com
Part A Getting Started 23
MP150 DLC Limitations
UDP is the default communication for MP150 units. An administrator password is required in order to access the
Ethernet network under Mac OS X. Without an administrator password, AcqKnowledge 4.0 can only be used in
the No Hardware mode for data analysis.

Disk Space
With any program, adequate disk space is necessary for storage of data files. Although BIOPAC saves files in a
format as compact as possible, some users may generate data files of several dozens of megabytes. To acquire
data for long periods (more than a few hours) while sampling at relatively fast rates (more than 1,000 samples
per second), as much disk space as possible should be available. (A removable drive may also be used). See the
Appendices for hints on working with large files.

Windows XP Compatibility
AcqKnowledge 4.3 is officially released for Windows 8, 7 and Vista operating systems, but testing was
performed with Windows XP. If AcqKnowledge

4.3 is installed on Windows XP, the user should not encounter


any systemic problems related to the operating system, except for Media and Tooltips.
Media functionality is not compatible with the XP operating system and performance will be problematic.
Tooltips may not be displayed on XP.
Sample Data is installed to < drive>:\Documents and Settings\All Users\BIOPAC Systems, Inc\AcqKnowledge 4.3

Mac Power PC Compatibility
AcqKnowledge 4.3 is officially released for Macintosh computers with Intel processor, but testing was also
performed on the Power PC. When AcqKnowledge 4.3 is installed on a Power PC, performance will be sluggish;
many of the Analysis operations will take several minutes or longer to complete.

Mac on Intel Compatibility
AcqKnowledge has been updated to a Universal Binary. This allows it to run natively on both PowerPC and
Intel-based Macintosh computers. AcqKnowledge also integrates directly with operating system features when
running on Mac on Intel-based computers, such as Automator and Spotlight.
Some features are not yet available for Mac on Intel-based computers due to the lack of third-party support.
These features include:
- MATLAB File Exchange (requires Mac on Intel support from MATLAB and The MathWorks).
o If MATLAB File Exchange is required, the application can be run in emulation mode by
checking the Open with Rosetta checkbox in the Get Info inspector of the Finder.

Contact BIOPAC Systems for more details on when these features may become available.
Spotlight Importer for Graph Files
Spotlight is an effective tool for searching for data. AcqKnowledge includes a Spotlight Importer that allows
Spotlight to extract and search information from AcqKnowledge graph files including: Graph title; Duration of
the recorded data in the graph; Text included in the Journal; Labels of data channels in the graph.
For example, if the names of subjects are recorded in a graph's Journal, Spotlight will be able to locate the graph
file based upon names extracted from the Journal. If enough information is kept in the channel labels and graph
journals, graphs can then be located and grouped using the Spotlight search features in ways not possible prior to
Mac OS X 10.4 and greater.
The Spotlight importer only supports files generated by Mac AcqKnowledge 3.7.0 or higher.
- Older Mac AcqKnowledge or any Windows AcqKnowledge files must be resaved to disk using a
compatible Mac AcqKnowledge file format.
AcqKnowledge 4 Software Guide
24 AcqKnowledge 4 Software Guide
Automator Integration and Scripting Support
Mac OS X 10.4 and greater includes a visual scripting environment called Automator. Automator allows for
drag and drop creation of Workflows. Each workflow is a series of steps that is performed in another
application. Each individual step is called an action. An action encapsulates a simple operation within another
application, such as opening a text file in TextEdit or applying a filter within Photoshop.
Over 40 actions have been written to allow AcqKnowledge to be controlled from Automator workflows. Using
these actions, workflows can be constructed to perform sequences of transformations, automating post-
acquisition analysis, performing experimental protocols, and other repetitive operations.
Workflows can be constructed using Automator. It is also possible to create, edit, and execute workflows directly
from within the AcqKnowledge environment using the new Workflow menu. The Workflow menu allows the
creation of workflows specific to an individual user account or to one shared by all AcqKnowledge users. These
workflows can then be edited in the Automator environment. Each workflow created using Workflow > New
Workflow will appear at the bottom of the Workflow menu each time AcqKnowledge is launched. By simply
selecting the name of the workflow from the Workflow menu, AcqKnowledge will execute the workflow.
Workflows executed from the Workflow menu should begin with either an Open Graphs or a Get Active
Graphs action. Workflows intended for use outside of the AcqKnowledge environment (e.g. used as Folder
Actions) should begin with a Launch Application action to start AcqKnowledge followed by an Open
Graphs or a Get Active Graphs action.
For more information about Automator and help constructing workflows, see the Apple website at:
http://www.apple.com/macosx/features/automator/
Visit the online support center at www.biopac.com
Part A Getting Started 25
MP System Features
In conjunction with your computer, the MP System is a complete system for acquiring almost any form of
continuous data, whether digital or analog. The MP System can perform a range of recording tasks, from high-speed
acquisitions to long duration acquisitions. Generally speaking, for physiological applications, the MP System is
limited only by the speed of your computer and the available memory or disk space. Features of the MP System
include:
Easy to use The MP System offers the same convenient and easy-to-use features which computer
users are accustomed to. Since the MP System (MP150 or MP36R) software runs under
these Windows and Mac OS environments, you can run other applications while you are
collecting data. In terms of hardware setup the MP System (MP150 or MP36R) uses
simple plug-in connectors and standard interface cables.
You dont need a degree in electronics to Set Up your system!
Flexible The MP System can be configured for a wide variety of applications, from single channel
applications to multiple-device measurements (up to 16 analog and 16 digital, or multiple
MP150s). You control the length of acquisition, the rate at which data is collected, how
data is stored, and more...all with a few clicks of the mouse button. Whether youre
measuring alpha waves or collecting zoological data, the MP System (MP150 or MP36R)
can meet your needs.
Menu flexibility You can easily customize menu displays to show only the functions you are using, thereby
reducing the risk of error or confusion in your lab. This function is extremely powerful for
laboratories working to GLP guidelines. It is also useful for teaching applications where
instructors can hide unnecessary menu items. See Appendix DCustomizing Menu
Functionality.
High Speed Sampling Sample rates up to 400 KHz aggregate
Arbitrary Sample
Rates
Apply different sample rates between channels or operate the STM100C stimulator at a
different rate than the acquisition sample rate
View & Control
Multiple MP150s
View and control multiple MP150 units over a local area network (LAN).
Calculation Channel
Presets
Customize your recording for specific measurements.
Template files AcqKnowledge Quick Start templates are available for over 40 applications. Just open
the template file and start the acquisitionappropriate settings are established for the
selected application.
Online Calculation Although the MP System provides an extensive array of measurements and
transformations you can apply to collected data, sometimes you need to perform
computations while data is being collected. The online Calculation functions allow you to
calculate new channels based on incoming signals. This feature allows you to compute
BPM, for instance, based on raw ECG data.
Online filtering Many times, it is preferable to filter data as it is being collected, rather than having to wait
until after the fact, so now you can apply filters to incoming data and view the results in
real time. That means online monitoring of data filtered to suit your needs.
Online measurements The MP System can instantly compute over a dozen measurements and computations for
any given data point(s). These options are available from pull-down menus and include
mean, peak-to-peak, value, standard deviation, frequency, and BPM.
AcqKnowledge 4 Software Guide
26 AcqKnowledge 4 Software Guide

Measurement
Validation
Validate measurements with the ValidateMeasurements.acq sample file that was
included with the software. The measurement definitions (page 92) include
measurement formulas and Sample data file explanations.
Preview your data Similar to chart recorders, the MP System allows you to change both the vertical
scale and the horizontal scale. You can change the amplitude scale or the time
scale to any value you wish, or you can have the MP System automatically scale
them for you.
Replace (or augment)
a chart recorder
Whether you want to replace a chart recorder or simply supplement an existing
setup, the MP System is fully compatible with most major recording devices.
Whats more, the MP Systemis compatible with most popular input devices, so
you can continue using the same transducers, electrodes and sensors.
Simplified editing It used to be that once your data was collected, the only way to edit it was with
scissors and adhesive tape. Now you can delete unimportant sections of your data
with a keystroke. You can paste together sections from different waves, or
simply edit out noise spikes from individual waves.
Append mode For some applications, data only needs to be recorded during some portions of a
long experiment. AcqKnowledge has an Append mode that lets you pause the
acquisition for as long as you wish, and resume the acquisition as many times as
needed. In this mode, you can start and stop a recording as you would with a chart
recorder. Appending data saves on storage space and processing time for
transformations.
Digital filtering All data contains measurement error and noise. Now you can reduce or eliminate
that error by using the digital filters and smoothing transformations included in
the MP System. You can smooth data across any number of samples, or filter out
noise from any frequency or bandwidth you wish.
Digital Output You can control external devices when an input or calculation channel meets
trigger conditions you specify. Use the Control channels to output a pulse when
the signal on an analog channel falls above or below a given threshold.
X/Y plotting You can view and acquire data in the form of an X/Y plot, with one channel on
the horizontal axis and another on the vertical axis. This allows you to explore
relationships between different channels and opens up a whole range of
applications, from chaos plots to respiration analysis to vectorcardiograms.
Histogram function You can easily examine the variability and the measures of central tendency of
any waveform data with the histogram function. Set the plotting options to suit or
let the software determine the best fit for graphing your data.
Math functions In many cases, simply collecting raw data is not enough. AcqKnowledge has an
array of built-in mathematical functions ranging from simple absolute value to
computation of integrals, derivatives, and operations involving multiple
waveforms (such as subtracting one wave from another). You can even chain
multiple functions together to form complex equations or expressions.
Annotation AcqKnowledge has a Journal you can use to append comments concerning your
input data, either online or after the fact. This is especially useful for noting the
characteristics of an acquisition (what was involved, what manipulations took
place, and the like) for future reference.
See also: Text annotation, page 58.
Visit the online support center at www.biopac.com
Part A Getting Started 27

Triggering If you need to measure response times or start data collection only after some
event has occurred, the MP System allows you to trigger an acquisition in a
number of different ways. You can trigger on the level of a signal, or with an
external synchronizing trigger.
Event marker Many times, especially during a long acquisition or in a laboratory setting, it is
useful to make a note of when specific events occurred so that these events (such
as when a manipulation occurred) can be recorded and any changes in the data
can be noted. The event function allows you to insert symbols in the record and
add text for each event. These can be added either while data is being collected or
after the fact. Event functionality can be automated for sequential application or
customized for Function keys.
File compatibility Data can be saved and viewed in a number of different formats. For word
processor programs like Microsoft Word

, use Copy to Clipboard and then paste


into the document. Use Save as Excel for Microsoft Excel

. You can output your


data in either text or graphical form, and AcqKnowledge can even read-in raw
data from a text file. Open (import) or save as (export) MATLAB and Igor Pro
Experiments, or raw (binary) data for low level exchange.
Pattern recognition Using an advanced pattern search/recognition algorithm, the MP System can
automatically find a specific pattern within waveforms. This is useful for finding
abnormal waveforms (such as irregular ECG waves) within a data file.
Cycle/Peak detection AcqKnowledge has a built-in algorithm to find cycle data, such as positive or
negative peaks, from any size data file. You can even search for all the
cycles/peaks with one command and automatically log statistics like time and area
to the journal.
Printing The MP System provides a range of printing options, and allows you to fit your
data on one page or many. You can print several graphs per page, even if you
only have one-channel recordings. Since MP System (MP150 or MP36R)s run on
Windows or Mac OS, no special printer drivers are required.
Report generation AcqKnowledge has many features to simplify report generation. Use the Journal
for notes and quickly copy and paste graph data or measurements to the journal or
to another program. Cascade event markers to prevent print overlap and select the
range of data to print and which options to display (measurements, event markers,
etc.). Use the Playback mode to simulate acquisition for presentations.
User Support Whether you have a question about compatibility with your existing equipment or
you need to develop a specialized measurement device, BIOPACs Applications
Department can address the problem.
AcqKnowledge 4 Software Guide
28 AcqKnowledge 4 Software Guide
Visit the online support center at www.biopac.com
Application Features
Use your MP System with AcqKnowledge software for a wide array of applications, such as:

Active Electrodes
Allergies
Amplitude Histogram
Anaerobic Threshold
Animal studies
Auditory Evoked Response
(AER)
Automate Acquisition Protocols
Automated Data Analysis
Automatic Data Reduction
Autonomic Nervous System
Studies
Biomechanics Measurements
Blood Flow / Blood Pressure
/Blood Volume
Body Composition Analysis
Breath-By-Breath Respiratory
Gas Analysis
Cardiac Output
Cardiology Research
Cell Transport
Cerebral Blood Flow
Chaos Plots
Common Interface Connections
Connect to MP System (MP150
or MP36R)s
Control Pumps and Valves
Cross- and Auto-correlation
Current Clamping
Defibrillation & Electrocautery
Dividing EEG into Specific
Epochs
ECG Analysis
ECG Recordings, 12-Lead
ECG Recordings, 6-Lead
EEG Spectral Analysis
Einthovens Triangle
EMG and Force
EMG Power Spectrum Analysis
End-tidal CO2
Episode Counting
Ergonomics Evaluation
Event-related Potentials
Evoked Response
Exercise Physiology
External equipment, controlling
Extra-cellular Spike Recording
Facial EMG
FFT & Histograms
FFT for Frequency Analysis
Field Potential Measurements
Fine Wire EMG
Forced Expiratory Flow &
Volume
Gait Analysis
Gastric Myoelectric Activity
Gastric Slow Wave Propagation
Gastrointestinal Motility
Analysis
Hardware Flexibility
Heart Rate Variability
Heart Sounds
Histogram Analysis
Imaging Equipment, Interfacing
Indirect Blood Pressure
Recordings
Integrated (RMS) EMG
Interface with Existing
Equipment
Interface with Third-party
transducer
Invasive Electrode
Measurements
Ion-selective Micro-electrode
Interfacing
Iontophoresis
Irritants & Inflammation
Isolated Inputs & Outputs
Isolated Lung Studies
Isometric Contraction
Isotonic Contraction
Jewett Sequence
Langendorff Heart Preparations
Laser Doppler Flowmetry
Left Cardiac Work
Long-term Monitoring
Lung Volume Measurement
LVP
Median & Mean Frequency
Analysis
Micro-electrode signal
amplification
Migrating Myoelectric Complex
Motor Unit Action Potential
Movement Analysis
MRI Applications
Multi-Channel Sleep Recording
Nerve Conduction Studies
Neurology Research
Noninvasive Cardiac Output
Noninvasive Electrode
Measurements
Nystagmus Investigation
Oculomotor Research
Off-line ECG Averaging
Online Analysis
Online ECG Analysis
Orthostatic Testing
Peripheral Blood Flow
Peristaltic (Slow Wave) Propagation
Planted Tissue
Pressure Volume Loops
Psychophysiology
Pulsatile Tissue Studies
Pulse Rate Measurement
Pulse Transit Time
Range of Motion
Real-time EEG Filtering
Real-time EEG Filtering
Recurrent Patterns
Regional Blood Flow
Relative BP Measurement
Remote Monitoring
Respiration Monitoring
Respiratory Exchange Ratio
Rheumatology
Saccadic Eye Movements
Sexual Arousal Studies
Signal Averaging
Simultaneous Monitoring
Single Channel Analysis
Single-fiber EMG
Software-controlled Stimulator
Somatosensory Evoked Response
Spectral Analysis
Spike Counting
SpO2 Analysis
Stand Alone Amplifiers
Standard Operating Procedures
Startle Eye Blink Tests
Startle Response
Stimulator, software-controlled
Systemic Vascular Resistance
Template Analysis
Tissue Bath Monitoring
Tissue Conductance Measurement
Tissue Magnitude & Phase Modeling
Tissue Resistance & Reactance
Ussing Chamber Measurements
Ventricular Late Potentials
Vestibular Function
Visual Attention
Visual Evoked Response
VO2 Consumption
Volume/Flow Loop Relationships
Working Heart Preparations


MP System (MP150 or MP36R) Application Notes
BIOPAC has prepared a wide variety of application notes as a useful source of information concerning certain
operations and procedures. The notes are static pages that provide detailed technical information about either
a product or application. A partial list of Application Notes follows. You can view or print application notes
directly from the Support section of the BIOPAC website www.biopac.com.
APP NOTE Application
#AH101 Transducer Calibration and Signal Re-Scaling
#AH102 Biopotential Amplifier Testing w/ CBLCAL
#AH103 Remote Monitoring System (TEL100C)
#AS105 Auditory Brainstem Response (ABR) Testing
#AS105b/c ABR Testing for Jewett Sequence
#AS108 Data Reduction of Large Files
#AS109 3-, 6-, and 12-Lead ECG
#AH110 Amplifier Baseline (Offset) Adjustment
#AS111 Nerve Conduction Velocity
#AH114 TSD107A* Pneumotach Transducer
#AH114b TSD107B* Pneumotach Transducer
#AS115 Hemodynamic MeasurementsPart I
#AS116 Hemodynamic MeasurementsPart II
#AS117 Pulse Transit Time and Velocity Calculation
#AS118 EMG Signal Analysis
#AS119 EMG Power Spectrum Analysis
#AS120 X/Y Loop Area Analysis
#AS121 Waveform Data Reduction
#AS122 Power Spectrum Analysis
#AH125 Pulse Oximeter Module Operation
#AH127 Precision Force Transducers
#AH128 Active Electrode Specifications and Usage
#AS129 Heart Rate Variability
#AH130 Blood Pressure Measurement
#AS131 Averaging Mode
#AH132 TSD105A Variable Force Transducer
#AH135 TSD117 Pneumotach Transducer
#AH136 BAT100 Instructions
#AH140 Angular Measurements with Goniometers
#AH141 Tri-Axial Accelerometer Calibration
#AS142 AcqKnowledge Rate Detector Algorithm
#AS143 Importing AcqKnowledge Data Into Excel
#AH144 Hand Dynamometer Calibration
#AH145 TSD101B Respiratory Effort Transducer
#AS148 Automated ECG Analysis
#AH149 O2100C Module
#AH150 O2100C ModuleSample application
#AH151 CO2100C Module
#AH152 CO2100C ModuleSample Application
#AH153 Physiological Sounds Microphone
#AH154 HLT100C High Level Transducer
#AS158 Analysis of Inspired and Expired Lung Volume
#AH159 TSD116 Series Hand Switch and Foot Switch
#AH160 Gas Analysis Module Response Time
#AS161 Automated Tissue Bath Analysis
#AH162 Stimulation Features
#AS168 Analysis of Intraventricular Pressure Wave Data (LVP Analysis)
#AS169 Speech Motor Control
#AH170 LDF100A Laser Doppler Flow Module
#AH175 Using the STMISOC Stimulus Isolator
#AS177 ECG Analysis using the Offline Averaging Mode
#AS183 VO
2
Measurement
#AH186 Psychological Assessment using the TSD115
#AH187 Electrodermal Response (EDR) using the GSR100 or TEL100
#AH190 Using the MCE100C Micro-electrode Amplifier
#AS191 Cardiac Output Measurement using the EBI100C and AcqKnowledge
#AH249 Online Averaging Latency Parameters (ISI, ABR)

30 AcqKnowledge 4 Software Guide
Chapter 2 AcqKnowledge Overview
Overview

The MP System software is called AcqKnowledge and performs two basic functions: acquisition and analysis.
The acquisition settings determine the basic nature of the data to be collected, such as the amount of time data
will be collected for and at what rate data will be collected. All of the acquisition parameters can be found
under the MP150 menu. The other menu commands pertain to analysis functions such as viewing, editing,
and transforming data.
Note: Minor differences exist between the Windows and Mac OS X screen displays and keystroke/mouse
functionality. These differences are noted throughout this section.
Menu Functionality See Page
File New, Open, Open Recent, Open for Playback, SMI BeGaze Import, Close, Save,
Save As, Save Selection As, Save Journal Text As, Send Email as Attachment, Page
Setup, Print, Quit
233
Edit Undo, Cut, Copy, Paste, Clear/Clear All, Remove Last Appended Segment, Insert
Waveform, Duplicate Waveform, Select All, Remove Waveform, Create Data
Snapshot, Merge Graphs, Clipboard (Copy Measurement, Copy Wave Data, Copy
Graph, Copy Acquisition Settings, Copy Data Modification History for All Channels,
Copy Data Modification History for Graph, Copy Focus Area Summary), Journal
(Paste Measurements, Paste Wave Data, Paste Acquisition Settings, Paste
Modification History for All Channels, Paste Modification History for Selected Channel,
Paste Focus Area Summary, Show Journal)
254
Transform operations that primarily modify the data in the graph
Recently Used, Digital Filters, Fourier Linear Combiners, Math Functions, Template
Functions, Integral, Derivative, Integrate, Smoothing, Difference, Resample
Waveform, Resample Graph, Expression, Delay, Rescale, Waveform Math
264
Analysis operations that derive data & measurements from the graph
Recently Used, Histogram, Autoregressive Modeling, Nonlinear Modeling, Power
Spectral Density, Autoregressive Time-Frequency Analysis, FFT/IFFT, DWT Discrete
Wavelets, Principal Component Analysis/Inverse PCA, Independent Component
Analysis/Inverse, Find Cycle, Find Rateplus a courtesy copy of the Specialized
Analysis package with classifiers and automation routines
295
Visit the online support center at www.biopac.com
Part A Getting Started 31
Display Tile Waveforms, Autoscale Single Waveform, Autoscale Waveforms, Optimize
Ranges, Overlap Waveforms, Compare Waveforms, Autoscale Horizontal, Zoom,
Reset Chart Display, Reset Grid, Adjust Grid Spacing, Set Wave Position, Wave
Color, Horizontal Axis, Show, Customize Toolbars, Channel Info, Preferences, Size
Window, Cursor Style, Create Data View, Organize Data Snapshots, Show All Data
Snapshots, Load All Data Into Memory
403
MP150
MP36
B-Alert*
BioHarness*
Set Up Channels, Set Up Acquisition, Set Up Advanced Averaging, Set Up Triggering,
Set Up Stimulator, Set Up Sound Feedback, Set Up Manual Event Insertion Keys, Set
Up Segment Labels, Show Input Values, Show Manual Control, Show Gauge, MP150
info, Update Firmware, AutoPlotting, Scrolling, Warn on Overwrite, Organize Channel
Presets, Set Up Linked Acquisitions, Exit Playback Mode, Manage Hardware
Connections
*Not all MP hardware menu items listed above will be available with B-Alert
BioHarness hardware.
103
Playback Replaces the hardware menu when Playback mode is active (use File > Open for
Playback and Playback > Quit playback to toggle playback and acquisition modes)
42
Window Controls the position of windows on the monitor 429
Help Provides online support files (PDF format and web links). 429
Media Capture or Playback media files(.avi, .wmv, or mpg) and synchronize with .acq data 431

AcqKnowledge 4 Software Guide
32 AcqKnowledge 4 Software Guide
Launching the AcqKnowledge software
The first step is to launch the software by double-clicking on the AcqKnowledge icon. If MP
hardware is not properly connected, you may receive connection messages resembling the
following examples.




If you receive a hardware prompt when you launch AcqKnowledge, there are two possibilities: You have not
properly connected everything and/or you have not powered up the MP System (MP150 or MP36R).
To use AcqKnowledge without an MP data acquisition unit (depending on the dialog,) choose
Cancel, Analyze Only, No Hardware, or set Preferences > Hardware > General to Always work
with no data acquisition hardware connected.

When AcqKnowledge is first launched, the user must pick an available MP150 unit from the Select MP150
Serial number dialog. The dialog lists all MP150 units that are powered ON and sitting on the same local area
network. If using more than one MP150 unit or working across a network, it will be necessary to lock/unlock
an MP150 to acquire data (see Appendix E on page 488 for details). The selected MP150 unit will be listed in
the upper left of the graph display as Connect to: if the Show/Hide Hardware toolbar icon is enabled.

Assuming everything is properly connected and there are no conflicts, AcqKnowledge will launch the Startup
Wizard. (AcqKnowledge 4.2 and higher only) Use this wizard to choose whether to create a new experiment,
open a saved graph for analysis or access the Help and support files.
Visit the online support center at www.biopac.com
Part A Getting Started 33

Startup Wizard under
Create and/or Record a new
experiment (Default)
Functionality
Create empty graph Opens new graph window for acquiring data with hardware. Combo box to the right
selects hardware type.
Open graph template from disk Brings up Open window for browsing to location of saved graph templates.
Use recent graph template Activates list of recently-opened graph templates for easy selection.
Sample graph template Activates list of sample graph templates stored in AcqKnowledge program folder for
easy selection.
Dont ask me again If checked, the Startup Wizard will not be presented upon next application launch.
Quit/OK Quits application or confirms selected operation.
Hardware type menu (center right of
screen)
If different hardware types have been previously added, they may be selected here
upon subsequent application launches. (If not, this menu will not appear.)
Open a graph file Presents similar options for analysis of existing graphs.
Help Launch various help and support options, including Web screencast tutorials.
NOTE: The Startup Wizard may be disabled if desired. (Display > Preferences > Other)
A window is the term used for the area on your computers screen where data is displayed and/or
manipulated. The graph window on the screen is designed to provide you with a powerful yet easy-to-use
interface for working with data.
At this point, you can use this window, create a new window, or open an existing window.
Its a good idea to create a new graph window for each acquisition. To create a new graph window after the
original launch, choose File > New.
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34 AcqKnowledge 4 Software Guide
Setting up channels
To configure the number of channels to be acquired during recording, select Set Up Channels from the MP
menu and choose View by Channels. This will generate the manually-configured Input Channels Setup
dialog.


If using AcqKnowledge
with BioHarness, Analog
channels can be turned
on/off but not changed.
- The default is to collect one channel of data on channel A1, and to plot and list values for this
channel. Usually, you will want to check all three boxes for each channel you acquire data on.
Acquire When the Acquire box is checked for a given channel that means data will be collected on that
channel.
Plot Determines if data will be plotted in real-time during the acquisition. If the plot box is unchecked,
data will be recorded, but the associated channel will remain hidden. The channel can be
unhidden by positioning the mouse pinter over the channel number box and Alt+clicking.
Value Enables you to use the Show Input Values window to display the values for each channel in real
time, numerically and/or graphically. These values are displayed in a separate window from the
main graph window.
Channel This is a dynamic alpha-numeric heading based on the type of channel selected: Analog (or
continuous), Calculation, or Digital. In the sample above, A1 indicates Analog channel one.
In contrast to analog data, Digital channels collect binary data that represent when a measuring
instrument is on or off. (For example, records whether a switch is open or closed, as in
reaction time studies or control applications.) Digital channels are acquired, plotted, and have
values listed the same fashion as analog channels.
Calculation channels are used for online computations and transformations of other channels.
These channels are Set Up just as analog and digital channels but also have additional dialogues
for you to specify what types of transformations and computations you would like to perform. For
a detailed summary of Calculation channel options, see the Calculation Channel section
beginning on page 117.
Label To the right of each channel number is an editable label for each channel, where you can type in a
label that identifies what each channel is measuring.
Preset Analog and Calculation channels include Presets as a quick way to get startedchoose a preset
and the software automatically sets the gain, offset, etc. appropriate for the selected application.
Choose from the list of available presets or create a custom preset; see page 108 for details.
Channel The channel sample rate is a function of the acquisition sample rate: all channel sample rate
Sampling options are equal to or less than the acquisition sample rate (as established via MP150
Rate > Set Up Acquisition). The options are a specific power of 2 less than the acquisition
sample rate. Channel sample rate info is included in the Display > Channel Info dialog. Use
the pull-down menu to set the channel sample rate. See page 109 for details.

Visit the online support center at www.biopac.com
Part A Getting Started 35
Setting up acquisitions

Once the channel parameters have been defined, the next step is to specify the acquisition settings. Choose Set
Up Acquisition from the MP menu to specify the type of acquisition to be performed. The basic parameters
involve:
a) How data should be collected and stored
b) The data collection rate
c) The acquisition duration (total length)
Storage Record and Append to Memory is the default acquisition option. Under this option, the MP System
automatically records data into a single continuous file, and stores the data in computer memory
(RAM) during the acquisition.
The third popup menu at the top of the dialog (which defaults to Memory) allows you to specify where
the data should be stored during the acquisition. You will probably want to choose Memory or Disk
storage. Computer memory (RAM) is usually faster (but less abundant) than disk space. If your
system uses any virtual memory, AcqKnowledge will use as much as possible. You may also store
data directly to the MP150 data acquisition unit, which can store 4 MB; you cannot store data directly
to the MP36R.
The advantage of storing to the MP data acquisition unit is that much faster
sampling rates may be obtained.
The disadvantages of saving data to the MP data acquisition unit are that there is
limited storage space and that data is not displayed on the screen while it is being
collected. When the acquisition has stopped, however, the data will be automatically
displayed on the screen.
The other option under storage is Averaging, which allows you to take repeated trials of the same
data. For more information on this feature, see the averaging section on page 157.
Rate Acquisition Sample Rate refers to how many samples the MP System should take each second. As
the MP System takes more and more samples per second, the representation of the signal becomes
more accurate. However, as the sampling rate increases, so does the demand for system resources
(memory, disk space, etc.). There is a point of diminishing return in terms of sampling rate for almost
all types of analog signals, where sampling above a given threshold adds relatively little information.
The MP150 sampling rate has a lower bound of 0.1 samples per second, and an upper bound of 400
kHz aggregate. The MP150 must use a pre-defined rate, it does not accept custom rates.
Choose the best acquisition sample rate from the pop-up list.
Note: Channel sample rates are variable based on the acquisition sample rate. All channel sample
rate options are equal to or a specific power of 2 less than the acquisition sample rate.
Duration The final acquisition parameter is Acquisition Length (Total Length), which controls how long an
acquisition will last. This can be scaled in seconds, minutes, hours, milliseconds or number of
samples. You can set this value either by entering a number in the acquisition length box, or by
moving the scroll box left or right.
Starting an acquisition
Once you have specified which channels will contain data and have defined the channel characteristics, the
next step is to start the acquisition. If a file window is not already open, choose File > New > Graph window.
Status
In the lower bar of the screen, next to the Start button, you should see a circular status light. The status light
indicates the communication link between your computer and the MP data acquisition unit.
AcqKnowledge 4 Software Guide
36 AcqKnowledge 4 Software Guide
Visit the online support center at www.biopac.com
If the MP data acquisition unit is properly connected to the computer and is turned on, the circle will be
solid and green.
If the MP data acquisition unit is not properly connected or not communicating with the computer, under
Windows OS the circle will be solid and gray and under Mac OS

X the circle may not appear at all or


a different symbol, such as double arrows, may be used if the application crashed during acquisition.
Start
To start an acquisition, position the cursor over the

button and click the mouse button, or select
Ctrl+ Spacebar. If there are no input devices (e.g., electrodes or transducers) connected to the MP System
(MP150 or MP36R), it will collect a small value of random signal noise with a mean of about 0.0 Volts.
For information on how to connect measurement devices to the MP System (MP150 or MP36R), see the
BIOPAC MP Hardware Guide.pdf.
To start an acquisition using a variety of triggers, see page 165.
Graphs that open without a Start Button
o Merge Graphs o Compressed Graphs
o Original Data Snapshot o Igor Pro Experiment
o Raw Data Files o PhysioNet
o Text Files o DWT, IDWT
o Transform menu operations: Off-Line
Averaging; Filter Response
o PCA, IPCA,
o ICA, IICA,
o Analysis menu operations:
Histogram; FFT (Magnitude and
Phase); IFFT; Rate (put result in new
graph option)

o AR Model separate graph output
o Nonlinear Modeling separate graph output
o HRV tachogram output
o Chaos > Plot Attractor
o Chaos > Detrended Fluctuation Analysis
o MatLab Graphs
Once an acquisition has started, the Start button in the acquisition window will change to Stop, and two
opposing arrows will blink, indicating that data is being collected. Also, the BUSY indicator light on the
front of the MP data acquisition unit will illuminate, showing that data is being collected.
Stopping an Acquisition
To stop an acquisition at any time, click the button or select Ctrl+ Spacebar.
An acquisition will stop automatically when it has recorded an amount of data equal to that indicated in the
Total Length box. To save this data file, choose File > Save.
Part A Getting Started 37
Display modes
The display modes are Chart, Scope, X/Y, Stacked Plot, and Playback. You may change the way data appears
on the screen at any time, even during an acquisition. To change the display mode, click the corresponding
icon in the toolbar.

Chart mode
Chart mode is the default display mode.
Chart mode plots data much as it might appear on a
chart recorder, with time on the horizontal axis.
Each channel of data is in its own track across the
screen, with borders between channels. The
waveforms will not cross boundaries into the tracks
of adjacent channels.
If a waveform is plotted off the scale of the channel
track, choose autoscale waveforms and
AcqKnowledge will select the best fit for
waveforms to their tracks.

Scope mode
Scope mode plots data much as it might appear on an
oscilloscope, with time on the horizontal axis.
Scope mode is similar to Chart mode, except that
there are no borders between different channels.
To help emphasize the selected wave in Scope
mode, select the Gray non-selected waves
Preference (via Display > Preferences).
Waveforms can overlap. The autoscale waveforms
command will automatically separate the waveforms
in the graph window.
Note: When only one waveform is present, the scope
and chart modes are identical.

X/Y mode
X/Y mode plots data from two channels against each
other, with the values from one channel on the
horizontal axis and the values from another channel
on the vertical axis. Plotting a channel against itself
displays a straight line.
X/Y mode can be useful for chaos investigations and
respiration studies.
Note: When viewing data in X/Y mode as it is being
acquired, plotting only the most recently
acquired data point can be a useful option. To
do this, select Display > Show > Dot Plot and
then Display > Show > Last Dot only.
Switching to X/Y mode during acquisition can be
slow. For best performance, switch to X/Y mode
either before starting the acquisition or after stopping
the acquisition.
AcqKnowledge 4 Software Guide
38 AcqKnowledge 4 Software Guide
X/Y mode continued
Plotted channels
- To change the channel being plotted: Click the Channel label once and hold.

X-axis, click above the waveform; Y-axis, click left of the waveform.
- To flip the axes: Click the button in the upper left.



- To change the channel label for this plot: Click the Channel label.

Toolbar icons
The center cluster of toolbar items is specific to X/Y mode. The left two buttons in this group are shortcuts
for the Autoscale vertical and Autoscale horizontal functions. Adjacent to these buttons are two buttons that
perform the center vertical and center horizontal functions.
Tools
Cursor: In X/Y mode, the I-beam tool in the lower right hand corner of the graph window changes into a
crosshair. When the crosshair is moved into the graph window, the coordinates of the crosshair are displayed
in the upper left corner of the graph window. The X value refers to the coordinate of the crosshair in terms of
the horizontal axis, and the Y value describes the location of the cursor in terms of the vertical scale. By
pressing the mouse, a crosshair is drawn over the closest data point and the measurement toolbar snaps to
that position to show the amplitudes of the actual pair of data samples plotted on the screen. In
AcqKnowledge 4.2 and higher, the Channel number and label are also displayed next to the measurement
values.

X/Y plot with ECG on X-axis and BPM on Y-axis
Autoscale: In X/Y mode, the Autoscale waveform function changes to read Autoscale vertical, which
plots the vertical channel so that it takes up two-thirds of the vertical channel space. This
function controls the height of the data being plotted in the graph window.
Similarly, the Autoscale horizontal function plots the waveform so that the waveform is
plotted in the center two-thirds of the window. This function controls the width of the data
being plotted in the graph window.
Visit the online support center at www.biopac.com
Part A Getting Started 39
Autoscale commands adjust the center point and the range of data displayed. To manually
change the scale, click in either the horizontal or vertical scale area. In this case, the scale at
the bottom edge of the graph windows (which usually reflects time) is the scale for the X
variable, and the vertical scale controls the scale for the channel plotted on the Y-axis.
Center: In X/Y mode, since only two channels can be displayed at a time, tile waveforms and
compare waveform are replaced with Center horizontal and Center vertical. These two Center
commands change the midpoint of the horizontal and vertical scales (respectively) so that the
midpoint of the scale is equal to the mean value (average) for that channel. These features are
useful for centering the display so that it is easier to interpret.
Ch. # Box: In X/Y mode, the channel numbering boxes are disabled.
Meas. Menu: In X/Y mode, the measurement popup menus are disabled.
Plot Recent Data Only

Use this option in X/Y mode to plot a user-defined amount of recent data. Checking the Plot recent data
only and entering a value will hide plotting for all data not included in the entered time value.

Plot recent data option not applied Plot recent data option applied with 6 sec. value

Stacked Plot mode
Stacked Plot displays multiple time ranges on top of each other and is enabled for acquisitions set to Append
(except when in X/Y mode). In this mode, all appended segments are stacked in the display, but only one
segment slice is active (selected). To view an individual segment, click the Chart mode icon.
Click the Stacked Plot mode icon to display the Stacked Plot controls beneath the toolbar:

To change the active slice, click the Jump Tool or the icon.

AcqKnowledge 4 Software Guide
40 AcqKnowledge 4 Software Guide
The selected segment is used for all enabled software functions. This means that autoscaling can easily create
what looks like a mess if the selected segment is not appropriate for scaling the largest segment. In compound
action potential graphs in Stacked Plot, the last segment slice will most often be the largest, so if you select
the last segment before autoscaling you will likely get the expected result. The Transform menu is disabled in
Stacked Plot mode.
A commonly used data visualization technique for examining the evolution of waveform morphology is the
2D waterfall plot or stacked plot. A stacked plot draws multiple traces for a single waveform on top of each
other, or slices. Each individual slice is a time-shifted plot of the original waveform. The slices toward the
bottom of the plot occur earlier in time then the slices toward the top.
Data can be acquired in stacked plot mode, but it is processor intensive. If acquisition setup includes high
sampling rates or control channels with low latency, acquire in chart or scope mode and switch to stacked plot
mode after acquisition.
The slices can be aligned at any type of events in the graph. This allows for alignment at appended segments
but also at locations found through other means. For example, an ECG waveform can be aligned at the start of
the T-wave to examine how the T wave evolves in time.
Active slice In stacked plot mode, there is a single slice that is called the active slice. By default
it is drawn in black; to change the color, select Stacked Plot Options > Drawing
Settings. The values on the axes in the graph, grid, displayed events and text
annotations, selections, and any transformations all apply to the active slice. The
active slice can be changed using the navigation buttons in the graph toolbar.
Vertical Separation The vertical separation between consecutive slices is expressed as a percentage of the
entire visible area. This percentage is kept constant through zooming and scrolling
operations.
Stacked Plot Options

Display > Show > Stacked Plot Options

Slicing Event

Drawing Settings
Use Stacked Plot Options to activate slices or visually distinguish the active slice from other slices being
drawn in Stacked Plot mode.
Automatic baseline Adjusts the baseline of each inactive slice to overlap the baseline of the active slice
prior to the application of any vertical separation. This helps compensate for baseline
drift in a signal. If it is disabled, no baseline compensation will be applied and the
stacked plot may exhibit visual vertical segment ordering problems resulting from
baseline drift (but in this mode can be used as a tool to examine basline drift).
Gray inactive slices Draws the active slice with a solid pen and draws inactive slices with a dashed gray
pattern pen. The gray pattern alternates pixels between the chosen waveform color
and the white background and has the effect of lightening the inactive slices, so you
may need to zoom in to see the effect.
Bold active slice Draws the active slice with a thicker pen. In step and line plot modes, plotting
normally occurs with a one pixel wide pen. Inactive slices will remain one pixel wide
while the active slice will have the thicker pen as indicated in the edit field. When the
waveform is in dot plot mode, the pixel width will be added to the waveform's default
dot size to increase the dot size for the active slice.
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Part A Getting Started 41
Change active slice Draws the active slice in a different color than the chosen waveform color. When
enabled, the same color is used for the active slice of each waveform in the graph.
The color can be changed by clicking on the colorwell to the right of the checkbox to
generate a standard color picker to select color.

Automatically jump You can use the Jump tool (green arrow) to change the active slice. Each time
the active slice is changed the left edge of the plot area will be changed to match the
start of the newly activated slice. When disabled, each time the active slice is
changed the display will be adjusted in such a way that the time interval between
slice starting positions and the display origin is kept constant.
Functionality in Stacked Plot mode
Autoscaling
When a graph is displayed in stacked plot mode, all autoscaling and related display operations (tile,
compare, overlap) will examine the visible data of the active slice only. It will not be possible to perform
autoscaling operations using the data of any inactive slice.
Autoscale Horizontal
In stacked plot mode, autoscale horizontal will make the active slice occupy the entire visible area. The
slicing event corresponding to the beginning of the slice will be placed at the left edge of the screen and
the next slicing event (or last sample point of the waveform if the active slice is the last slice) will be
placed at the right edge of the screen. The vertical offset will remain unaffected.
Data Views
Different data views may have independent Stacked Plot settings. All settings are independent including
drawing preferences, slicing events, vertical separation, and active slice settings. Stacked plot settings are
stored individually for each data view in the graph file and will be restored when the graph file is opened
from disk.
Any graph-wide operation that may affect the active slice will update all data views that are configured to
use stacked plot mode. This includes operations that affect the data (e.g. transformations) or events (e.g.
waveform editing).
Graphs Containing No Slices
It is possible that graphs may not contain any slices whatsoever if no events match the slicing event
criteria. If a graph in Stacked Plot mode contains no active slices, it will be drawn as if the graph was in
regular chart mode with the following differences:
All data is drawn using any active slice settings given in the stacked plot drawing options.
The Active slice index will read N/A.
The previous/next/choose slice graph toolbar buttons and Display > Show > Stacked Plot Options menu
items will be disabled.
It will be possible to view all data from t = 0 to the final data sample of the graph using the horizontal
scrollbar.
All autoscaling operations will function as if chart mode was active. Autoscale horizontal will make all of
the data of the selected waveform visible on screen.
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If the table of available slices was being displayed prior to the removal/editing of the last matching slicing
event, the table will be emptied and the OK button dimmed. The cancel button will remain active for
the table window to be dismissed.
The slicing event, vertical separation, and drawing menu items and toolbar controls will remain active.
Playback Mode (Replay)
Playback mode will replay a graph file stored on disk in real time to
simulate acquisition. Analog, digital and calculation channels are
replayed as stored in the graph file, but in AcqKnowledge 4.2 and higher,
calculation channels can be reconfigured to reproduce online calculation
channels that have no offline equivalents. Calculation channels from the
original graph can be modified, extended, or removed without affecting
the data stored on disk in the original graph file.
1. Select File > Open for Playback.
2. Locate a graph file and then click Open.
3. A new graph window will be generated.
The Connected to: hardware menu will indicate that the
graph will be acquiring data from the specified file and the
Start button will change to a Replay.
4. Press Replay to begin playback.
Button alternates with STOP, cant pause.
5. Select Playback > Quit Playback Mode to return to acquisition
status.

Use Open for Playback to
experiment with different
calculation channels settings on
the same data or to recreate an
experiment for demonstration
purposes.
Playback mode has millisecond timing accuracy and allows for reconfiguration of most acquisition
parameters. Exceptions include:
Length is limited to the amount of data in the file
Acquisition Sample Rate is fixed (use Channel Sample Rate to downsample)
Number of analog and digital channels is fixed
Save last, MP, and Averaging modes are disabled
Append will replay the same data.
Do not record data while playing back a data file. If one data file is open in "Playback" mode and is
'replaying' and a second data file is open in MP150 mode and is acquiring data, clicking back and forth
between graph windows causes the MP150 menu to flip to the Playback menu (even though 'Connected to'
shows communication with an MP150 unit).
See the AcqKnowledge Demo file under the Help menu as a sample of data playback.

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Part A Getting Started 43
AcqKnowledge 4 Software Guide
Data Views
A Data View window is used to provide an alternate view of the same data. You can present data in two or
more modes for comparison, such as X/Y plots and chart plots. To compare responses in real time, turn off
Autoplot in one Data View (e.g., Dose 1) and continue Autoplotting in another (e.g., Dose 2).
To create a new Data View for the active (selected) graph, choose
File > New and select type Data View or
Display > Create Data View
This will generate a new window displaying the active graphs data, and will name the new window Data
View of Filename .
TIP Use the Jump-to tool (see page 57) to correlate data views.
Data Views share fundamental data characteristics such as channel labels, events, and sampling rates, but can
be customized for the following:
autoscrolling horizontal scale, precision, and offset
channel button display state vertical scale, precision, and offset
wave color measurements, including number of
rows, precision, visibility, and use of
interpolation
event display state
channel order
grid settings, including spacing,
visibility, and locking state
plot mode
channel drawing mode (step, line, or dot,
including dot plot size and type)
selected area
autoplotting
hardware connected to display
hidden channels
The Data View window can be used like any other graph window. The menus and controls can be used to change
how the data is presented. An acquisition can be started or stopped in any of the Data Views for a graph, and any
transformations performed on the data in the Data View will be reflected in the graph and all of the other Data
Views. Printing a graph from a Data View will use the display settings of that Data View for outputting the graph.
When a file is saved to disk, the display configuration of any Data Views that are open are saved into the graph
file. When the graph file is reopened, all of the Data Views and their display settings will be restored.
Data Views are saved with the data file only if they are open at the time the original graph is closed and
saved.
Closing a Data View causes this view to be lost; it is not saved with original file.
Closing a Data View that was previously saved with a data file will not be saved if the data file is saved
after closing the Data View.
Closing a Data View will not invoke a warning that the Data View will not be saved.
Original Data Snapshot is not merged into the newly created data file.
In AcqKnowledge 4.3 and higher, a selected area can be shared across multiple Data Views by clicking and
holding the left mouse button over the I-beam toolbar cursor and choosing the Link Selections Between Data
Views option. (See example figure below.)

44 AcqKnowledge 4 Software Guide
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Analysis
For purposes of illustration, you should open an existing file that contains actual data.
Sample files were installed with the software. Select File > Open and choose a file from the
list in the dialog.
After opening the file called demo data.acq, the screen should resemble the following
sample file display.

Sample File Display
The sample graph displays six different types of data, and there is a border between the waveforms.
To the left of each waveform is a vertical strip containing a text string that can be used to help identify each
waveform.
The time scale along the bottom denotes when the data was recorded relative to the beginning of the acquisition.
Only the last eight seconds of the total data record are visible, although the file contains
the complete record.
The data displayed on the left edge of the graph represent events that occurred about 22
seconds into the record, and the data displayed at the right edge of the screen represent
events that occurred about 30 seconds after the acquisition was started.
The maximum vertical scale range is from +10 to -10 Volts.
This reflects the maximum input voltage the MP150 unit can accept and is a greater
range than you will usually encounter.
The display scale can be adjusted to virtually any value range, as demonstrated in the
graph window above.
As indicated by the horizontal scale, only a few seconds of data are displayed on the screen. If you choose
Statistics from the Display menu, you can determine the total length of the record.
To view data that was collected earlier in the record, you can use the horizontal scroll bar to move to different
points in the record. The horizontal scroll bar allows you to move around in a data file, just as the scroll bar in a
word processor allows you to move to different points in a document.
Alternatively, you can position the cursor in the horizontal scale area (where the numerical values are listed) and
click the mouse button. This will generate the following dialog (see page 71 for details).
Part A Getting Started 45

The Time scale box allows you to change the amount of data that appears on the screen at any given time. In the
sample dialog, this is set to 2 seconds per division. The divisions on the screen are indicated by the four vertical
lines, thus displaying eight seconds at a time (two seconds per division times four divisions). By entering a larger
value in this box, more of the record will be displayed on the screen at any given time. Conversely, entering a
smaller value in this box will cause a shorter segment of data to be displayed on the screen. (Above screenshot is
from AcqKnowledge 4.2)
To display the entire waveform (in terms of duration), a shortcut is to choose Autoscale horizontal from
the Display menu. The Autoscale horizontal command fits the entire data file into the window, regardless
of the total length of the acquisition.
The Initial time offset box lets you jump to a different point in the time display. Changing the value in this box
allows you to display data beginning at a certain point in the record. For instance, if you want to see the data at the
beginning of this record, you would tell AcqKnowledge to display data with an initial offset of 0 seconds, which
would result in the following:
As you can tell
from the time
scale, the first
data displayed (at
the left edge of
the screen) was
collected at the
beginning of the
acquisition. Also,
the scroll box has
moved to the left,
indicating that
the data on the
screen represents
data collected
earlier in the
record.
If you click in the horizontal scale area again, the same dialog will appear, and this time the value in the start box
should have changed to reflect the new section of data being displayed on the screen.

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AcqKnowledge also allows customization of the vertical
scaling, or amplitude, of each waveform. Clicking the
vertical scale area produces a dialog (see page 72 for
details).
The vertical scale dialog allows you to change the range
of amplitude values displayed (scale) and set the value
that appears in the center of the vertical scale (midpoint).
You can vary the midpoint and apparent magnitude of
each waveform by changing the values in each box. By
changing the value in the scale box, a smaller value has
the effect of increasing the apparent amplitude. Entering
a number about half the current value will cause the
amplitude of the wave to appear to double.
- ScaleIn the sample dialog, the units are set to 2
Volts per division. As with the horizontal scale,
there are four divisions on the vertical axis, so
this setting should show 8 Volts range of data.
- MidpointThe box below this controls the midpoint of this range. In this case, the midpoint is set to 2
Volts, which means that this channel will display the range from - 4 Volts to + 8 Volts.
As with the time scale, you can have AcqKnowledge automatically come up with the best fit in terms of midpoint
and units per division. To do this, select the Autoscale waveform command from the Display menu, and the
amplitude and offset of each wave will be adjusted to fit their sections.
Any changes you make in terms of rescaling (either horizontal or vertical) will only affect the way data is
displayed, and will not change the basic characteristics of your data file.

Selecting a waveform
Although all four waves are displayed at once, you may want to operate on only one channel at a time. To do this,
you need to select the channel you wish to work with. Selecting a channel allows you to highlight all or part of
that waveform, and enables you to perform transformations on a given channel.
In the upper left corner of the graph window there is a series of boxes that represent each channel of data. The
numbers in the boxes correspond to the channel used to acquire the data (the specifics of setting up channels are
discussed on page 34). In the sample waveforms shown previously, ECG channels are represented by channels 1
and 2, with respiration on channel 4 and blood pressure on channel 5.
To select one of these channels
- position the cursor over the channel box that corresponds to the channel you wish to
select and click the mouse, or
- position the cursor on the waveform of interest and click the mouse.
Part A Getting Started 47
Show/Hide Channel
To hide a waveform, press ALT for Windows or OPTION for Mac and click the channel box.
To view a hidden waveform, repeat the appropriate key-click combination.

Zoom
Another way to examine data is to use the zoom tool. The zoom tool allows you to select any portion of any
wave and magnify it as much as possible. To use the zoom tool, click the icon in the lower right portion of the
screen. As you move the mouse into the graph area, you will see it change from an arrow to a crosshair (+).
Start by positioning the cursor in one corner of the box, holding down the left mouse button, and dragging the
crosshair horizontally, vertically, or diagonally to form a box which encompasses the area you need to zoom in
on. When you release the mouse button, AcqKnowledge will automatically adjust the horizontal and vertical
scales. To unzoom, choose Zoom back from the Display menu.

Select an area
Once you have selected a channel, you can edit parts of that channel by selecting a section of the waveform.
The options available to you include cutting, copying, and pasting sections of waveforms. You can also transform
and analyze entire waveforms or specific sections of waveforms.
For any of these functions, you will need to select (or highlight) an area to be operated on. If you want to select a
section of a waveform, position the cursor over the icon in the lower right hand corner of the screen and click
the mouse button. Now move the cursor to the first point in the area that you wish to select. As you move the
cursor into the graph area, you will see it change from an arrow cursor to a standard I-beam editing tool.
To highlight a section of a waveform, position the

cursor at the left edge of the area you wish to select and
hold down the mouse button. Now move the mouse to the right until you have selected the desired area.
To select more than one screen of data, position the

cursor at the left edge of the section to be highlighted,
then click and hold the mouse button. Use the scroll bars to move to a different point in the record, and when you
reach the desired endpoint (right edge) of the selected area, hold down the Shift key while you position the cursor
and click the mouse button. Selecting an area this way will also allow you to fine tune the selected area to
include only a specific range of data.
Once a channel has been selected and a section of that area highlighted, you can operate on and edit that section of
the waveform. The editing commands behave much the same way as the editing functions in a word processor.
You can cut, copy, delete or paste sections of data as defined by the selected area. In most cases (depending on
available memory) you may undo an edit by choosing Undo from the Edit menu, or by using the shortcuts CTRL
+ Z for Windows or +Z for Mac.
Selecting a portion of a waveform also allows you to apply transformations to a particular area, rather than the
entire area or all waveforms. Selecting an area also allows you to take snap measurements for parameters such as
delta T, mean, standard deviation, frequency, and so forth. The measurement options are discussed in the next
section.
The Selection Palette (Display > Show > Selection Palette) can also be used to select an area.
Keyboard data selection
Keystroke combinations can similarly used to select or deselect graph data on a sample-by-sample basis. This
helps add an enhanced level of precision to the selection operation. See data selection keyboard shortcuts on the
following page. (AcqKnowledge 4.2 and higher)
Keyboard Shortcut Description
Windows: Shift + Ctrl + Left Arrow
Mac: Shift + Command + Left Arrow
Subtracts one sample interval from the right edge of the selection. If the selection is
empty, no action is performed.
Windows: Shift + Ctrl + Right Arrow
Mac: Shift + Command + Right Arrow
Subtracts one sample interval from the left edge of the selection. If the selection is
empty, no action is performed.
Shift + Left Arrow Adds one sample interval to the left edge of the selection.
Shift + Right Arrow Add one sample interval to the right edge of the selection.
Left Arrow Moves the selection one sample to the left, constructs a zero width selection.
Right Arrow Moves the selection one sample to the right, constructs a zero width selection.
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Transform data
AcqKnowledge includes a library of functions to transform data or perform
mathematical calculations on waveform data. All of these options can be found under
the Transform and Analysis menus, and are discussed in detail in the Analysis section
beginning on page 295.
When performing transformations
- If a section of a waveform is highlighted, the transformation will apply to
that section.
- If no area is selected, AcqKnowledge will always select a single data point.
- If the transformation can only be performed on a selected area (digital
filtering, for instance) and a single point is selected, the entire waveform
will be used (and the transform entire wave option will be disabled; close
out of the dialog and select an area if desired).

Measurements
Once you have selected a channel to work
with, you can quickly and easily take
measurements on each wave. The
measurements appear in the row of boxes
across the top of the graph window. You can
specify the number of measurement boxes to
show and the display precision in the
Preferences dialog of the Display menu.
Each measurement consists of three parts: (a)
the channel selection, (b) the measurement
function, and (c) the result or actual
measurement value.
In this example, results for the selected channel (SC) are:
Time 17.28 sec
delta t 0.00000 sec
freq 0.10157 Hz
bpm 6.09446 BPM.
The pull-down channel selection allows you to calculate a measurement either for the selected channel (SC) or
from a numbered channel in the record. To switch between the channel options, click in the channel window. The
pull-down menu shows the channel numbers and labels for all channels in the file. By default, each measurement
will reflect the contents of the selected channel.
The pull-down measurement menu allows you to choose between different types of measurements. To choose a
measurement, click the measurement popup menu and select a measurement from the list.
- Some measurements (such as Time or Value) look at only a single data point whereas other measurements
(such as mean and delta T) examine a range of data on the selected channel.
- Some of the measurements that depend on a selected area (such as delta T) look at differences in the
horizontal axis measurement whereas other range measurements (such as peak-peak) use the vertical scale
information in calculating measurements.
For a complete description of each of the measurement functions, turn to page 88.
The final component of a measurement window is the measurement result.
- When an area is selected (or if the selected area is changed) the measurement result automatically updates
to reflect the change.

Part A Getting Started 49
Events (Markers)

In many instances it is useful to have the software mark an occurrence
or event during an acquisition so it can be referenced later. For
instance, you may want to note when a treatment began or when an
external event occurred so you can examine any possible reaction.
The software uses Events, which are marked in the data to record
events.
Event markers can be pre-established and automated. Event icons and labels appear at the top of the graph
window, and can be edited, displayed, or hidden from view.
You can automatically insert event markers during an acquisition by pressing the Esc key. This will insert a
event at the exact time the key is pressed and will activate the text line entry so you can immediately enter a
comment to be associated with the event.
For a detailed description of events and event functions, including options to pre-establish event labels and set
function keys for different labels, see Set Up Event Hotkeys (page 202).
See also: Text Annotation, page 58.

Grids

Grid superimposes a set of horizontal and vertical lines on the graph window. The grid is designed to allow for
easy measurements, since the grid lines correspond to horizontal and vertical scale divisions. The grid can be
locked (analysis, printing) or unlocked (visual aid).
To activate the grid display, choose Display > Show > Grid or click the toolbar icon.
To display minor grid lines, use Ctrl- .
To customize grid line and color and optimize the display and print features, choose Display > Show > Grid
Options.
For more information about using and printing grids, see page 75.
Note: The Scale dialogs change when grid lines are locked. See page 71 for details on Horizontal Scale and page
72 for details on Vertical Scale.
Horizontal Split View
Horizontal Split View is a tool for splitting the data in a single graph into two simultaneously viewable areas
and displaying them side-by-side for convenient viewing. Split View is available for data plotted in scope, chart
or stacked plot modes. Both views can contain independent time scales, initial offset and autoscroll settings. This
can be useful for making side-by-side comparisons of data at different time ranges, or for reviewing the same
section of data in two separate time scales for more detailed examination. Split View configurations and scalings
can be saved and restored in the graph.
Split View can be activated via the following methods:
Choosing Display > Split View. This divides the graph into two equal regions with independent time scales,
and the bar in the center can be dragged to the desired location.
Clicking the Split View bar in the horizontal scale area. The Split View bar is indicated by
the appearance of a double-arrowed cursor when the left border of the horizontal time scale
is moused over. After the cursor appears, hold and drag the cursor to create the desired
Split View.
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In the above example, the view in the left pane was rescaled independently of the view of the same data on the
right pane. This enables a closer view of an area of interest while maintaining the original data display. If a Split
View encompasses any events, annotations or focus areas, these will be visible in both panes.
Note that events, annotations, selected areas and focus areas appearing in the Split View are duplicate
displays of the same items. If any of these items are added, modified or deleted in one view, this change
will also be applied to the other view.
Split View is not supported in XY mode.
Printing of Split Views is not currently supported within the BSL application. If printing is desired, save the
graph in *.jpg format or use standard operating system screen capture utilities.
To exit Split View, uncheck the Display > Split View option or drag the Split View bar back to its home position
at the left of the horizontal scale.

Autoscroll Horizontal Axis Controls
During data acquisition, three plotting modes are offered. These are normally accessed via the MP menu, but can
be more easily dialed in by using the button in the lower right of the horizontal axis region. This button
toggles between the following modes, and the button display changes to reflect the plotting type selected.
Status Icon Description
Manual

Horizontal axis is not modified by application during data acquisition. Only manula
adjustments affect the data plot. Equivalent to unchecking both MP > Autoplotting and MP >
Scrolling.
Sweep

Data is plotted until it reaches the right edge of the graph. At this point the data is scrolled,
clearing data display and showing the newly acquired data starting at the left edge. This
mimics the sweep of an oscilloscope. Equivalent to checking MP > Autoplotting and
unchecking MP > Scrolling.
Autoscroll

New data is plotted at the right edge of the graph. When new data is acquired, existing data is
scrolled to the left, creating space to plot new data. Equivalent to checking both MP >
Autoplotting and MP > Scrolling.

Part A Getting Started 51
Journals
The Journal is a general-purpose text editor built into AcqKnowledge that works like an electronic notepad for
recording notes and data and saving text and/or numeric values for later review. The Journal can be used at the
same time data is being acquired. Every graph file has a graph-specific Journal file permanently linked to it. There
is also an option to generate independent Journals for data view, use with multiple graphs or protocols.
Graph-specific journalJournal is saved with graph;
preferable for retaining notes and analysis within a
graph file. Display settings are independent. To save
a graph-specific Journal independent of its graph,
use File > Save Journal Text As option.
Independent JournalJournal is saved into its own
file, separately from graphs; preferable when
performing analysis on multiple graphs at the same
time. Independent journals allow multiple journal
windows to be open at the same time (each graph
view can have its own journal associated with it), but
only one Independent Journal can be used at a time.
For more information on using Journals, see Journal Details on page 80.
Saving data
Once data has been collected, it can be saved as a file and opened later. The data file can be moved, copied,
duplicated and deleted just like any other computer file. By default, files are saved as AcqKnowledge (.ACQ)
files, which are a proprietary format designed to store information in a format as compact as possible. Although
these files can only be opened from within AcqKnowledge, the data in these files can be exported either as a text
file or as a graphic image.
Exporting data to a text file allows you to examine the data using other programs, such as a spreadsheet or
statistical analysis package. Saving data as a graphic (.JPG) enables you to work with the data in graphic format.
One of the most useful applications of this is the ability to edit and place AcqKnowledge data as it appears on the
screen. You can use this feature to paste graphs into word processors, drawing programs, and page layout
programs. To learn more about these options, turn to the Save As section beginning on page 244.
Format change warnings
When a file save function requires a format change for compatibility or alters file content, a prompt will be
generated to require the user to confirm the option to update format or convert and save.


Created with a previous version of AcqKnowledge Windows PC AcqKnowledge format


Saving as a Graph Template will erase all data Imported from another file format

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Data Snapshot Embedded Archive
Data Snapshots are essentially embedded archives of the original acquired data that are stored with the graph
file so you can easily view them together at a later time to compare results to original waveforms or intermediate
stages of analysis.
IMPORTANT Archive functions do not create a new filethey are not backup functions.
Original data is copied and pasted to the end of the original file.
You cannot use this feature to recover lost or damaged original data.
There are two ways to create a snapshot:
1. Automatic after acquisition: Display > Preferences > Other > Create Data Snapshots after acquisitions

When this is enabled, a date-stamped archive of the data in the graph when acquisition stopped is created.
In Append mode, the entire graph is archived with each Append, old data as well as the newly acquired
data.
This is a memory intensive function;
each archive that is added to a graph file
will increase its size on disk by
approximately 40%. When prompted,
click OK to proceed.
2. Manual: Edit > Create Data Snapshot

A snapshot is then taken of the data at that point in time and stored with the graph. Manual archives allow
you to preserve intermediate stages in a complex analysis for future reference. You will be prompted for a
comment to describe the archive. This description will be used in the header when you display the archive.
To view the embedded archive(s) associated with a graph file, choose Display > Show All Data Snapshots.
This will open a new graph window for each archive associated with the graph. The time portion of the Filename
for each graph is from the computer clock (saved with semi-colons because you cannot save a file with colons in
the filename). The Data Snapshot from graph will open with no Start button.
Manual Archive: description and time
Original file
Automatic Archive: time only
Snapshots will also retain the following in addition to the data:
- Events - Text annotations
- Graph-specific journals
- AcqKnowledge GLP Modification logs (ACK100W-G and ACK100M-G only)
Part A Getting Started 53
Print
AcqKnowledge allows high-resolution printing of
hard-copy graph plots much as they appear on-
screen.
- To print a file, choose Print from the File menu.
This will print the contents of the screen on the
selected printer.
- To print the entire file, choose Autoscale
Horizontal from the Display menu first.
- You must print a journal as a separate command
from print graph file.
You may instruct AcqKnowledge to print the
contents of a file across several pages by entering a
value in the Fit to box. Entering 4 in this box, for
instance, will place the length of the page evenly
across four pages when printing.
Print options are available after you click OK in the
initial File > Print dialog; see page 252.



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Chapter 3 User Interface & Context Menu Features

Vertical axis scaling buttons Toolbars
Long channel labels and units Keyboard Shortcuts
Graph window tooltip improvements Mouse Controls
Menu item tooltips Custom toolbars for transformations and analysis
Channel Info Toolbar position retention and changes
Transformation history Event tool enhancements
Canceling Transformations Typed event label drawing improvements
Transformation Progress Bar Choose MP150 Help Button
Focus Areas Button Transparency
Customizable Chart Track Dividers
Plotting Background Colors
Toolbars
Many of the most commonly used features in AcqKnowledge can easily be executed
with a mouse click. The toolbars contain shortcuts for some of the most frequently
used AcqKnowledge commands.
Choose Display > Show or right-click outside the data window and enable Toolbars in
the context menu. Click an icon to activate it; icons are grayed out when they are not
applicable.
Toolbar positionToolbars for Measurements, Channel number, and Hardware
revert to the default location when a file is opened (position is not retained).
Part A Getting Started 55
Toolbar

ICON FUNCTION

Change display to scope mode.

Change display to chart mode (default).

Change display to X/Y mode.

Toggle Stacked Plot (overlap segment) mode; see page 39X.

Autoscale selected waveform only.

Autoscale waveforms along the horizontal axis.

Center waveforms vertically in the active window.

Center waveforms horizontally in the active window (X/Y mode only).

For channels that have range information, set the vertical scale to match the maximum allowable
input signal for the MP unit

Find the peak of a selected area.

Find the next peak (after peak has been defined).

Click and hold the mouse to produce a list of graph (.acq) files in the current folder.

Show/Hide selection palette (AcqKnowledge 4.3 and higher)

Show/Hide gridlines in the graph window. Click and hold the mouse to display various grid preset
options.

Show/Hide Hardware Connected to: in the graph display; also functions via Display > Show >
Hardware.

Show/Hide measurement pop-up windows.

Show/Hide channel selection boxes.

Channel selection boxes appear above the data window and indicate the channel(s)
being used to record data.
To select a channel, depress the corresponding channel number box (CH 1 is selected here).
To hide a channel, Alt-click (PC) or Option-click (Mac). A slash mark will cover the channel
box and the channel will be hidden.

Show/Hide graph textual value display in toolbar. When enabled, adds real-time display of
channel amplitude values above the graph. Right clicking
brings up a textual value toolbar preferences dialog. See page 73 for more textual value details.
Show/Hide events (markers) and enable Event toolbar icons:

Text Annotation display; see page 58.

Show/Hide graph-specific journal (MacJournal must be open for icon to work).

GLPrequires installation of AcqKnowledge GLP (Good Laboratory Practice)

Rewinddeletes the last recorded segment. Alt+Rewind (Windows) or Option+Rewind (Mac
OS X) deletes all recorded data, similar to the Append Reset button.

Open the customize toolbar menu.

Toggle display of the Media Capture viewer.

Toggle display of the Media Playback viewer.
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Hardware Toolbar

The hardware toolbar displays connected to information and includes quick access to add/change hardware.
The Hardware toolbar reverts to the default location when a file is opened (position is not retained).
Also functional through the Toolbar icon.
Cursor Toolbar

By default, the cursor tool icons are in the lower left corner of the graph window, but are dockable to any
desired location. These cursor tools are used in many of the on-screen functions described below, including
editing, measurements, and the amount of data displayed.
The cursor tools are also accessible via the Display menu (Display > Cursor Style)
CURSOR TOOLBAR

This is a general-purpose arrow cursor tool, used for selecting waveforms, scrolling
through data, and resizing the chart boundaries between waveforms when in chart mode. All
other cursors default to this mode when the cursors are moved outside the graph area. Use
Alt-click to step through the channels; each click makes a new channel active. The arrow
cursor can also be activated by the Ctrl+B keystroke.
In AcqKnowledge 4.2 and higher, holding down the left mouse button with the arrow tool
positioned over a graph channel will activate a single data point, which displays as a solid
black vertical line. This is known as spot measurement mode. Dragging the mouse will
then update selected measurement values to the new horizontal locations of the arrows
position in the graph. The mouse button should be depressed for approximately 0.5 seconds
in order for spot measurement mode to become active. Releasing the button restores the
arrow cursor to its normal status.

This is a standard I-beam editing tool. This tool is used to select an area of a waveform (or
waveforms) to be edited or transformed. To select it, click the middle button in the lower
right hand corner of the screen. Now move the cursor toward the waveform. Youll notice
that the cursor changes from an arrow to an I-beam when it is placed over the graph area.
Using this tool to edit data is analogous to editing text with a word processor.
When this cursor appears, you can select an area of data by holding down the mouse button
and dragging the mouse to either the left or right. You can extend the selected area to include
data that is not on the screen by positioning the cursor at the left edge of the area to be
selected and clicking the mouse button. Next, use the scroll bars to scroll through the data
until the desired data appears on the screen. Hold down the shift key while you position the
cursor to select the right edge of the area to be selected. Click the mouse button to select the
area. To extend the selection, hold the Shift key and move the cursor or the arrow keys. The
I-beam cursor can also be activated by the Ctrl+I keystroke.
Clicking and holding on the I-beam tool will generate a pop-up menu for displaying the
Selection Palette or linking selections between Data Views.
Visit the online support center at www.biopac.com
Part A Getting Started 57
CURSOR TOOLBAR


When Link Selections Between Data Views is selected, the standard I-beam cursor icon
will change to one with a link appearing across it. When enabled, any area selected in a Data
View or source graph will also be applied to any other associated data view. For more
details, see Data Views on page 43.

This is a standard zoom tool. The zoom tool lets you select and magnify any portion of any
wave. Click the icon to use the zoom tool. As you move the mouse into the graph area, it
will change from an arrow to a crosshair (+). Start by positioning the cursor in one corner
of the box, then hold down the (left) mouse button and drag the crosshair horizontally,
vertically, or diagonally to form a box that encompasses the area you need to zoom in on.
When you release the mouse button, AcqKnowledge will automatically adjust the horizontal
and vertical scales. To unzoom, choose Zoom back from the Display menu.
Hold the Alt key to change the zoom mode to zoom out ( in the magnifier). The zoom
tool can also be activated by the Ctrl+G keystroke.
Grid
Control

Adjust the grid lines horizontal and vertical. Hold the option key for locked grids to drag to
the end.
Event
Definition

Inserts an event at the mouse click location. See page 209 for Event details.
On a plot, the horizontal location matches the x coordinate of the click
In Chart mode, the event will be placed on the channel track where the click took
place.
In Scope mode, the event will be defined on the active channel.
Within the events bar, clicks define global events.
When Event Definition is active, the cursor changes to a flag and the cursor includes a
downward pointing arrow to indicate where the event will be defined.
The Event Definition tool is disabled in X/Y mode and if events are not visible.
Event
Removal
Zap

Deletes event(s) from a graph with the mouse. It allows for quick editing to eliminate
misclassified events found through visual inspection.
If the user clicks on a single event, that event will be removed from the graph.
If the user clicks and drags to define a rectangular area (similar to the zoom tool), all
events between the left and right edges of the area will be removed; the event icon does
not need to lie vertically within the bounded area in order to be removed.
When Event Removal is active, the cursor changes to a lightning bolt.
Jump-to

Data views and advanced analysis output display multiple representations of the same data at
the same time. Sometimes this association may be abstract or difficult to visualize. The
Jump-to tool is a green arrow, and is available in all display modes and during acquisitions.
Use the Jump-to tool to correlate data.
- Click the Jump tool on a data point to jump all of the open data views for that
graph to the same time.
- Click the Jump tool on a point in an X/Y plot to jump data views in chart or scope
mode to the point in time corresponding to the point in the X/Y plot. This can be
useful for correlating PV loops back to other acquired signals.
- Rate analysis output graphs will jump back to the corresponding point of source data
at the start of that cycle.
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CURSOR TOOLBAR
- Clustering scatterplots will select the appropriate segment of the source graph
corresponding to the chosen data point.
- Change the active segment in Stacked Plot mode; once a trace is selected the display
will adjust to show the new active segment.
Text
Annotation

Use Text Annotation to add floating text notes on top of data in a graph; the text notes move
and scale with the data. During report or figure preparation, it is nice to be able to add
additional textual information on top of signals to help clarify signals for readers or draw
their attention to particular areas of visual interest. AcqKnowledge provides a text annotation
facility to assist in figure preparation.
Click the A icon and then click in the graph window to generate the Text Annotation
Contents dialog. Drag the red handles from the annotated text to add connector lines to
connect the text to the data.

Text
Annotation

continued






Connector handles

Add a range

Resize a range

Move a connector
Visit the online support center at www.biopac.com
Part A Getting Started 59
CURSOR TOOLBAR

Text annotations are short pieces of text that float above channel data and can be used to
draw visual attention to particular areas of interest in a graph. These text annotations can be
simple outlined text, can have a connector from the outline boundary to a specific sample
point on the waveform, or have a range indicator of a specific width. Each text annotation is
tied to a sample of data in a channel; when the data is moved by coping, pasting, or other
waveform editing operations, text annotations remain fixed to their corresponding sample
positions, similar to channel events.
Although text annotations are tied to horizontal locations like events/markers, they are
displayed in a relative fashion. The relative pixel distance between the text annotation outline
boundary and the sample of data remains the same under zoom and autoscaling operations.
- For example, an annotation that is 20 pixels above a T-Wave peak position will
continue to be drawn 20 pixels above regardless of zoom. This allows for flexible
data viewing while maintaining text annotation visibility.
Text annotation controls
Create Insert using the text annotation cursor tool. With the tool active, click in
the graph to define a new annotation.
Select Click an annotation once to select it.
Reposition Drag a selected annotation to reposition it.
Add Connector Connectors or range indicators can be added to selected annotations by
using the editing handles on the edges of the selected annotation.
Edit Connector If the selected annotation has a connector to a data point of the graph, an
editing handle will appear on the end of the connector. The connector can
be moved to a different data sample of the graph by dragging the editing
handle on the end of the connector to the new position in the channel. To
remove the connector, grab the editing handle on the end of the connector
and drag the mouse inside the text annotation.
Range Indicator If the selected annotation has a range indicator, editing handles will
appear at both ends of the range indicator. To resize the range indicator,
grab an editing handle and move the mouse. To remove the range
indicator, grab an editing handle and move the mouse back inside the text
annotation.
Autoposition Resizing windows or adding channels may reposition text annotations
outside of the visible area. Click and hold down the text annotation tool to
activate the text annotation popup menu. The Autoposition Hidden
Annotations option automatically repositions all annotations so they are
visible.

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CURSOR TOOLBAR
Clear all Click and hold down the text annotation
tool to activate the text annotation popup
menu. The Clear annotations option will
clear annotations for a selected channel or
for all annotations. This action cannot be
undone so you will be prompted to
confirm your selection:

Selection palette

Many of the tools within the AcqKnowledge environment are based around the selection. The selected range
of data in the graph is used as the source for measurements, waveform editing, transformations, and other
operations. The Selection Palette is a floating dialog that can be used to precisely enter the selection. See page
412 for Selection Palette guidelines.
Start/Stop toolbar
toggles to
Channel Number Toolbar
Toggles the display of channel number and label region. The
Channel Number toolbar reverts to the default location when a file is
opened (position is not retained).
.
Also functional through the Toolbar icon.
Events toolbar

Select an event to enable the toolbar. Use the arrows to move
forward or backward through all event marker types. Click the event
palette icon to generate the event palette.
Focus Area Toolbar

Use the Focus Area feature to isolate portions of data that are of
particular interest within a graph. Focus Areas can be defined,
added, labeled and deleted within any portion of the graph. For more
details on creating and using Focus Areas, see page 86.
Visit the online support center at www.biopac.com
Part A Getting Started 61
Measurements toolbar

Click the down arrow for quick access to measurement preset
functions, including pre-loaded options for organizing
measurement rows and columns. Or create and save custom
measurement display presets by choosing New Preset, entering a
name for the preset and clicking OK.
Right-click in the measurement bar for quick access to options for
copying measurement and using linear interpolation. The
Measurements toolbar reverts to the default location when a file is
opened (position is not retained).
Custom toolbars for transformations and analysis
AcqKnowledge 4.1 and above allows users to construct new
toolbars for triggering transformations and analysis. An arbitrary
number of toolbars may be created and populated with buttons
that can trigger any menu item in the Transform and Analysis
menus. The contents of the text-only buttons match the menu
item title. These toolbars will persist for each user and their
positions and visibility within the graph window will be retained.
Transformation toolbars may be accessed via the "Customize Toolbars" button next to the rewind
button.


Toolbar position retention and changes
Toolbars can be rearranged within the graph
window or detached and turned into floating
tool windows. Any modifications made by
the user to the position of most toolbars
within the graph window will be stored as an
application preference and used for new
graph windows as they are created and graph
files that are opened from disk; however,
toolbars for Measurements, Channel number, and Hardware will revert to the default location when a file is
opened (position is not retained). Default toolbar positions have changed to move the Start button and cursor
tools to the top of the graph window; users preferring the ordering in previous versions may manually
reposition the toolbars. Toolbar Tooltips may be deactivated when toolbars are detached from a graph.
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Axis Controls

If axis controls interfere with scale values,

adjust the opacity slider in Preferences > Graph

to hide the icons until the cursor passes over them
.


A scaling button acts as a shortcut for opening the grid and visible range dialog, similar to double-
clicking the axis. If a channel corresponds to an analog channel that has calibration steps, a calibration
wrench button be displayed and will open the hardware calibration dialogs. This allows visual access
to commonly used operations for channels.

Module dependent: Generate the scaling or calibration dialogs for the channel input or calculation.
Analog inputs will open to the scaling dialog and channels that require calibration will initiate a repeat
calibration routine.


Use Display > Channel Info or use the channels contextual menu to display the Channel Information.

Toggle the lock icon at the right edge of the window to change the lock state of the grid for horizontal
axis or the channel. Unlocked is open (latch to right); locked is closed.
Enable cursor tools during acquisitions
Enables access to cursor tools while recordings are in progress. (AcqKnowledge 4.2 and higher only, Display
> Preferences > Graph)
Button Transparency
Scaling, calibration, transformation history, and grid lock buttons may be made semi-transparent to allow
units, axis values, and other information underneath the buttons to remain visible. The Preferences > Graph
panel includes an Axis controls slider to change drawing from fully transparent to fully opaque.
When the mouse is within the buttons, they will be drawn fully opaque regardless of transparency setting. The
transparency is shared by the scaling, calibration, transformation history, and grid lock buttons and is the
same for all open graphs as this is an application-level preference.
Customizable Chart Track Dividers
Users may change the color used to draw the dividers between channels tracks The Preferences > Graph panel
contains "Chart Track Divider Appearance" options.
Visit the online support center at www.biopac.com
Part A Getting Started 63
Plotting Background Colors
Starting with AcqKnowledge 4.2, customizable background colors for individual graph channels are available
in Preferences > Graph > Plotting Background Colors.
Spectrum Analyzer Palette
The Spectrum Analyzer Palette provides a dynamic display of the frequency
decomposition of data, in real time or post-acquisition.
See page 415 for details.


Keyboard shortcuts
Menu Option Windows OS Mac OS X
Program info Help > About AcqKnowledge AcqKnowledge menu
Quit Ctrl + Q Q
Hide AcqKnowledge minimize (corner box) H
File menu
New Ctrl + N N
Open Ctrl + O O
Open for Playback
SMI Begaze Import
Close Ctrl + W W
Alt+left-click to close all
Save Ctrl + S S
Save As
Save Selection As
Save Journal Text As
Send E-Mail Attachment
Page Setup
Print Ctrl + P P
Quit Ctrl + Q
Edit menu
Undo (when applicable) Ctrl + Z Z
Cut Ctrl + X X
Copy Ctrl + C C
Paste Ctrl + V V
Clear (journal) Delete key none
Clear All
Remove Last Appended Segment Use the Rewind toolbar icon
Insert Waveform
Duplicate Waveform Ctrl + D D
Select All Ctrl + A A
Remove Waveform
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Menu Option Windows OS Mac OS X
Create Data Snapshot
Merge Graphs
Clipboard
> Copy Measurements
> Copy Wave Data
> Copy Graph
> Copy Acquisition Settings
> Copy Data Modification History for
All Channels
> Copy Data Modification History for
Selected Channels

Ctrl + K
Ctrl + L

Ctrl + U

Journal
> Paste Measurements
> Paste Wave Data
> Paste Graph
> Paste Acquisition Settings
> Paste Modification History for All
Channels
> Paste Modification History for
Selected Channels
> Show Journal

Ctrl + M
Ctrl + /
Ctrl + J

M
Transform Menu
Recently Used
Digital Filters
Fourier Linear Combiners
Math Functions
Template Functions
Integral
Derivative
Integrate
Smoothing
Difference
Resample Waveform
Resample Graph
Expression
Delay
Rescale
Waveform Math
Analysis menu
Find Cycle Ctrl-F F
Find Next Cycle Ctrl-E E
Find All Cycles in Focus Areas
Visit the online support center at www.biopac.com
Part A Getting Started 65
Menu Option Windows OS Mac OS X
Find All Cycles Ctrl-R R
Find In Selected Area
Find Rate none none
Display menu
Tile Waveforms
Autoscale Waveforms
Overlap Waveforms
Compare Waveforms
Autoscale Horizontal

Ctrl+Y


Ctrl+H

Zoom Back
Zoom Forward
Ctrl + - (minus key)
Ctrl + = (equal key)
-
+
Reset Chart Display
Reset Grid
Adjust Grid Spacing
Set Wave Positions
Wave Color
Horizontal Axis
Show
Customize Toolbars
Channel Info
Preferences
Size Window
Cursor Style
Create Data View
Create Focus Area
Organize Data Snapshots
Show All Data Snapshots
Load All Data Into Memory

M150 menu
Set Up Channels
Set Up Acquisition
Set Up Advanced Averaging
Set Up Triggering
Set Up Stimulator
Set Up Sound Feedback
Set Up Manual Event Insertion
Hotkeys
Set Up Segment Labels
Show Input Vales
Show Manual Control
Show Gauge
Select MP150
MP150 Info
Update Firmware
Autoplotting
Ctrl + ]
Ctrl + [
Not supported in AcqKnowledge
4.0. Supported in 4.1.1 4.3










Ctrl + T













T
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66 AcqKnowledge 4 Software Guide
Menu Option Windows OS Mac OS X
Scrolling
Warn On Overwrite
Organize Channel Presets
Set Up Linked Acquisitions
B-Alert Headset Check Impedance
B-Alert Headset AMP Baseline
B-Alert Headset Brain State Gauges
Check for Hardware
Exit Playback Mode
Manage Hardware Connections




Licensed functionality
Licensed functionality
Licensed functionality

Start/Stop Acquisition Ctrl + spacebar Ctrl + spacebar
Delete recorded data
Delete all recorded data, similar to the
Append Reset button.
Ctrl+Rewind button Option+Rewind button
Window menu
Bring All to Front

Help
Application Notes from Web
Open AcqKnowledge Manual
Open MP Hardware Guide
Open AcqKnowledge Tutorial
About AcqKnowledge

Cursors
I-beam
Arrow (pointer)
Zoom
Grid
Event
Jump to
Annotation

Ctrl-I
Ctrl-B
Ctrl-G

I
B
G
Horizontal Scroll Location

Home

End

Page Up

Page Down
In chart, scope, or stacked plot mode (i.e., all but X/Y)
these keyboard shortcuts can be used to scroll to various
parts of the graph.
Jumps to t = 0 (i.e., places first sample of data flush with
left of graph window)
Jumps to the end of the currently selected waveform (i.e.,
places last sample of data of the selected waveform flush
with right of graph window)
Scrolls backward in time one full screen (i.e., places
leftmost sample of previous visible area at the right of the
new visible area).
Scrolls forward in time one full screen (i.e., places
rightmost sample of previous visible area at the left of the
new visible area).
Visit the online support center at www.biopac.com
Part A Getting Started 67
Mouse Controls
Contextual menu items correspond to the AcqKnowledge main menu state.
Application menu customization has a corresponding effect on contextual menu display. If a contextual menu
item does not have a corresponding application menu item, the menu customization file identifier will begin
with IDM_CM.
The following options can be accessed with a right-click for Windows or Control-click for Mac.
Mac OS X only: If the mouse is over a portion of the graph that has a context menu available, the
cursor will change to an arrow with a menu.
Graph window

Journal window



Horizontal Scroll

Vertical Scroll

Display

Measurements

Events
Mouse Scrollwheel Support
The scrollwheel operates on whatever window is underneath the mouse; this window does not need to be the
topmost window. Many third-party mice include scrollwheels, scrolling balls, or trackpads to allow for quick
access to navigating through a document. Mice may provide two separate controls, one for scrolling vertically
and one for scrolling horizontally.
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AcqKnowledge supports horizontal and vertical scrolling using the scrollwheels on the mouse. Scrolling is
supported in graph windows, journal windows, the event list in the event palette, and a number of other
dialogs and windows that contain scrollable lists. A dynamic zoom operation can easily be performed in an
AcqKnowledge graph channel by holding down the Ctrl key (PC) or the Option key (Mac). Scroll up to
zoom in and down to zoom out. (Zoom operation supported in AcqKnowledge 4.2 and higher)
- Mac OS X: To increase the scroll speed, hold down the Option key while using the scrollwheel.
Transformation history
Transformation history functionality provides the ability to track transformations that are performed on
channel data. This gives a visual indicator of whether transformations have been applied to a channel and a
record of the sequence of transformations and the parameters for the transformation. The history for the
channel is viewed in the "Channel Info..." dialog. This dialog is accessible via the Channel Info option of
the context menu or the Display > Channel Info menu item. This dialog replaces the "Statistics" dialog used
in earlier versions.
Cancelling Transformations & Transformation Progress Bar
In AcqKnowledge 4.1 and higher, transformation cancel support has been restored to the software to offer
Cancel buttons in progress dialogs that indicate the completion status of threaded transformations.
Progress dialogs have also been enhanced so the textual message includes a graphical progress bar with
the percentage that is completed. If the progress message does not contain a percentage, an indeterminate
progress bar will be displayed.
AcqKnowledge 4.1 and higher extends the analysis package to display dialogs while analysis routines are
in progress. This progress dialog contains a cancel button which may be used to terminate the analysis
before it is complete.
The event tool allows events to be inserted on a graph with the mouse. When performing event editing,
three new context menu shortcuts have been added to help make the process quicker:

Assign Current Event Type: Right-click an area with no data to set the type of event that will be
inserted on the next left-click of the mouse.
Event Palette: Toggles event palette displays.
Edit event: Right-click a specific event to open the event palette to Selected Event controls for the
event that was right-clicked.
Typed event label drawing improvements
The Event system has been enhanced to allow different drawing options for channel-specific events when
they are drawn in the data plotting area. These drawing options are applied to event labels, event
amplitude markings, and event time location text. The following drawing options may be customized:

Font (including family, size, italic/bold, and other options)
Rotation angle of text baseline
Text alignment (left, center, right)


Visit the online support center at www.biopac.com
Part A Getting Started 69
Choose MP150 Help Button
A Help button is available in the "Choose MP150" dialog that appears when the application is attempting
to locate an MP150, either on initial application installation or on communications errors. The Help
button opens a "Troubleshooting MP150 Communications.pdf" document from the application's User
Support System. This troubleshooting guide provides common information from Technical Support for
decoding the network blink states of the MP150 and other steps to take to troubleshoot why the MP150
and computer cannot communicate properly.
Tooltips
Channel label and units length and tooltips
Character length limitations for channel label and units have been expanded: labels may now be up to 1032
characters and units may be up to 511 characters. Tooltips have been added to display the full channel units
when the vertical axis is moused over. Tool tips do not wrap, so long labels may extend beyond the visible
viewing area of the computer monitor.

Graph window tooltip improvements
Several of the toolbar buttons and the Start/Stop button in the graph window are associated with keyboard
shortcuts that may be used instead of the buttons. Tooltips for these toolbar buttons display the corresponding
keyboard shortcuts. Toolbar Tooltips may be deactivated when toolbars are detached from a graph.

Menu item tooltips
Menu item tooltips display informational text about how menu items may be used. (Similar text was
displayed in earlier versions of AcqKnowledge for Windows in the status area and in earlier versions of
AcqKnowledge for Mac as Balloon Help). Analysis menu tooltips have been expanded to provide more detail
regarding the types of analysis that are performed by the selected item.
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Chapter 4 Editing and Analysis Features
Overview
This section provides a brief overview of some of the most frequently used AcqKnowledge features and
functions. For more detailed information about specific features, turn to Chapters 9 through 13.
If you are not currently running AcqKnowledge, double click the AcqKnowledge icon to start it. Choose Open
from the File menu and select the file called demo data.acq. Your screen should look like this:

Edit menu functionality during acquisition
The following Edit menu functions may move or alter memory and cannot be performed during acquisition:
Undo, Cut, Clear, Clear All, Paste, Insert Waveform, Duplicate waveform, and Remove Waveform.

Scroll bars
As you can see, there are four channels of data in this file (Heart Rate, ECG, EEG, Resp, EMG Raw, EMG,
Integrated EMG). Although this record is 30 seconds long, only a few seconds are displayed on the screen at
one time. You can move to different locations in the record by moving the scroll box at the bottom of the
screen. Dragging the box left moves you to earlier points in time, and moving right displays events closer to
the end of the record. Clicking on the arrows at either end of the horizontal scroll bar allows you to move to
different points in time at smaller increments.
A vertical scroll bar is on the right side of the screen, and. If you click the scroll arrow at the top of the box,
youll see that one waveform appears to move down within its track on the screen. Moving this scroll box
changes the amplitude offset of a selected channel. As with the horizontal scroll bar, you may either move the
box or click the arrows.
Visit the online support center at www.biopac.com
Part A Getting Started 71
Scaling
Horizontal axis
Click the horizontal scale (above the scroll bar) to generate a dialog where values can be entered for units
per division and horizontal scale offset.

Time Scale
The time interval (units per division) between the on-screen grid marks. There are four vertical divisions
per screen, and the default is 2.00 seconds per division, so eight seconds of data will be displayed on the
screen display. Entering a larger value will display more of the record, and entering a smaller value will
display less.
Initial offset
The time corresponding with the first data point displayed. For example, to display the middle 1/3 of the
data file (assuming the record is 30 seconds long), set the offset to 10 seconds and the seconds per
division to 2.5 seconds.
Precision
Controls number of decimal places following whole units appearing in the horizontal axis.
Hold Relative Position for Append acquisitions
This option is available in AcqKnowledge 4.2 and higher, and active only in Append acquisition mode.
When checked, the display for appended acquisitions will show the same relative position with respect to
the start of acquisition. This is convenient when doing short-duration; high-speed acquisitions where you
want to be able to zoom in on the signal of interest and have the relative position (from the start of
acquisition) stay the same. If the acquisition is started with the horizontal scale such that it falls between
acquisition segments, this feature is not implemented.
When Hold relative position is checked; after zooming in on a section of data that has been selected
(highlighted) and is completely within one appended segment, the scale of the selected area changes with
each appended segment such that it remains relative to the start of acquisition for that segment and
updates the measurements. If the selected data area falls within two or more appended segments, this
feature is not implemented.
Global Grid Settings
Opens dialog for applying master grid settings for all channels. For more details, see Grids on page 75.
Channel Grid Settings
Opens dialog for selectively applying grid settings to one or more channels. For more details, see Grids
on page 75.

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Vertical (Amplitude) axis

Clicking the mouse in the vertical scale area (where the amplitude of each channel is displayed) generates
the Set Screen Vertical Axis dialog, where values can be entered for units per division and vertical scale
offset.
Scale
Determines the limits of the viewable vertical axis scale (usually Volts). AcqKnowledge divides each
channel into four vertical divisions. When data is displayed in chart mode, each track is divided
into four divisions. When data is displayed in scope mode (or if there is only one channel of data) the
entire screen is divided into four intervals. To increase the apparent amplitude for a given channel, set
this value to a smaller number; entering a larger number will cause the waveform to appear to have
less variability.
Midpoint
Refers to median displayed value for a particular channel. A checkbox to the left of each of these
options allows you to apply these scaling options to all channels. By default, the scaling options you
choose will only apply to the channel indicated in the dialog. If you want to apply these to all
channels, click all the checkboxes.
Precision
Controls number of decimal places following whole units appearing in the vertical axis. Can be
applied to selected or all channels.
Apply to all channels
Applies settings selected in the various dialog options to all channels.
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Part A Getting Started 73
Adaptive Scaling
Adaptive scaling uses the data to automatically determine the appropriate visible range for the data.
As the data changes or the baseline shifts, the visible area shifts along with the data to ensure that data
will always be plotted on the screen. Rather than limiting data visibility to a fixed voltage range, the
range adjusts for factors such as background noise, electrode movement, EMG interference,
disconnection, etc.
Adaptive scaling can be applied to channels individually and can be unique for each Data View. A
settings button is activated when to Use adaptive scaling is enabled.

Scaling changes will be applied whenever the domain of the plot area is changed. This includes
manual changes to the horizontal scale, horizontal scrollbar use, horizontal auto-scrolling when
dragging out a selected area, auto-scrolling or auto-plotting during acquisition, initial enabling of
adaptive scaling and auto-scrolling when executing Find Cycle/Peak functions.
Show Textual Value Display
This option enables a real-time display of the most recently acquired values on a channel-by-channel
basis, providing amplitude information akin to clinical monitoring displays. This can be useful for
obtaining a quick visual numerical summary of incoming data while a recording in progress.

In post-processing, the value display can be seen by performing a spot measurement (clicking the
arrow cursor on a single data point).
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Textual value display in spot measurement mode
Textual value display can be customized for font, color and style, and positioned at the top or bottom
of any selected channel. These options can be configured independently per channel or applied to all
channels.
- In chart and stacked chart modes, the value display will appear for all enabled channels.
- In scope mode, the value display will appear only if the selected channel has the value display option
enabled.
- Textual value display is not supported in XY mode.
To enable textual value display:
Click on the vertical axis area to open the setup dialog and enable the Show textual values display
checkbox. Use the Settings button to set the font style, size and color.

Channel Grid Settings
Opens dialog for selectively applying grid settings to one or more channels. For more information,
see Grid Details on page 75.

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Part A Getting Started 75
Grid Details
You can customize the grid behind the waveforms displayed in graph windows in a number of ways.

Grid Lock/Unlock
Each scale has a small padlock in the lower right
hand corner that displays the current state of the
grid lock for that axis and channel. Click the
padlock to change the lock state.
Unlocked gridthe number of grid lines
and their pixel spacing on screen is kept
constant through zoom and scaling
operations
Locked gridthe grid lines themselves
are maintained at constant values through
zoom operations, e.g. a grid line which is
located at .753 volts when the grid is
locked will continue to be located at .753
volts regardless of changes in scale.
Grids can be locked and unlocked on individual channels.
The lock for the horizontal axis is shared by all channels.
The vertical scale can be locked and unlocked independently.
The lock state of the grid can also be changed through the axis dialogs displayed when the mouse is clicked
on the axis scale values in the graph window.
Click the Lock units/div checkboxes.


NOTE: All grid screenshots are from AcqKnowledge 4.2.
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Grid Scaling
When the grid is locked, the scaling factors controlling how much data is visible on the screen (the distance
between consecutive major lines of the grid and a fixed location for one of the lines of the grid) are specified
differently. When the grid is unlocked, these scaling factors do not affect the grid.
The Grid Spacing option specifies the scaling factors and whether or not to Show minor divisions on the
grid display. Changing these values only affects the grid display, not how the waveform is scaled.

Vertical grid: the total range of vertical units displayed per track is specified (Major division) along with
the first value that should be displayed (First grid line).
Horizontal grid: the scaling factors are specified in how many seconds of data should be visible on the
screen (Major division) and the time offset of the left hand side of the display (First grid line).
Settings can be applied to a selected channel or all channels. (Controlled by checking or unchecking
Apply to all channels).
Adjust Grid Spacing
To modify the horizontal and/or vertical grid spacing, choose Display > Adjust grid spacing. This will
generate the aforementioned dialog for modifying the locked axes of the selected waveform. (Lock vertical
grid and Use channel specific horizontal grid must be enabled in order for the gridline fields to become
active). Enter the desired values and click OK.
Settings can be applied to a selected channel or all channels. (Controlled by checking or unchecking
Apply to all channels).
The following Grid items can also be selected by right clicking with a graph channel and using the contextual
menu.


Grid: Toggles Grid display on and off.
Adjust grid spacing: Use to change Grid spacing
for one or all channels (divisions between
gridlines and position).
Grid Options: Use to change Grid display for one
or all channels (Color, width, style, dash length,
dash spacing, and scale adjustment position).
Grid Preset: Use to select/create /save custom
Grid presets and organize them in a list. (left)


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Part A Getting Started 77
Example of channel specific horizontal grid


Note in figure on left, the horizontal time scale division is
one second per division in the graph channel, but two
seconds per division in the horizontal axis. (Green bar area)







Horizontal Axis Grid Controls

Global Grid Settings: Brings up dialog specifying grid settings used in the shared Horizontal Axis of
the graph.
Channel Grid Settings: Brings up the Adjust grid spacing dialog referred to on previous page.
Individual channel-specific grid settings take priority over the Global Grid Settings. If no channel-specific
grid setting exists, the Global settings are applied.
Grid Tool

The Grid Tool allows divisions of the grid to be specified with the mouse. This tool has four states:
Inactive The cursor changes to a circle with a line running through it. The grid
cannot be adjusted since both the horizontal and vertical axes are unlocked.
Horizontal axis locked The cursor changes to a horizontal line. A mouse click and drag will change
the location of the horizontal lines of the grid.
Vertical axis locked The cursor changes to a vertical line. The tool can be used to adjust the
vertical spacing of the grid.
Both axes locked The cursor changes to a crosshair. The rectangle of a full grid division can
be drawn over the data. Adjust the spacing of locked grid lines underneath
the waveform.
If the Alt (PC) or Option key (Mac) is held down for the Grid Tool in any of the active
modes, an ellipsis will appear under the cursor. After a mouse click or drag, a Grid Settings
dialog will be generated. This dialog is functionally similar to the grid dialogs accessible via the
axis settings dialogs.
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Based on lock status, the dialog will allow you to adjust Horizontal, Vertical or combined settings.
The values displayed in the dialog correspond to the grid ranges that were just drawn out on the screen
with the grid tool if a mouse drag occurred.
If the mouse was simply clicked, the current grid settings are displayed.
This dialog allows the grid drawn out with the grid tool to be made more precise.
Grid Reset
To return to the original grid, choose Display > Reset grid.
This will reconstruct the default, unlocked grid of four divisions per screen with solid light gray grid lines.
Grid Options
The major and minor grid lines can be further customized with spacing, number of divisions, and different
colors and dashing styles. These are modified under the dialog generated via Display > Show > Grid options.

Line color Click the color well to generate a color chooser.
Line width Adjust the corresponding slider.
Dash style Select a style (solid or broken) from the pop-up menu.
Dash length Adjust the corresponding slider (for any dash mode that is not a solid line).
Spacing Adjust the corresponding slider (for any dash mode that is not a solid line).
# of Divisions Enter a value in the text field to set the maximum number of minor grid lines
to be displayed in a single major grid division.
Apply visual settings to all channels
When checked, the visual settings for major and minor grid lines are applied to all
channels. When unchecked, the settings will be applied to the selected channel only.
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Part A Getting Started 79
Scale Adjustment
Select whether to use Start/End or Range/Midpoint parameters to determine
horizontal and vertical scale adjustments. Applied only when grids are locked.

10 sec. Horizontal Scale adjustment set to Start/End parameters

10 sec. Horizontal Scale set to Middle Point/Range parameters
To undo your selections and return to the original grid, choose Display > Reset grid. This will reconstruct
the default, unlocked grid of four divisions per screen with solid light gray grid lines.

Friendly Grid Scaling
Too much precision can create numbers that are difficult to quickly interpret, so friendly grid scaling
adjusts the range to the nearest possible whole numbers. For example, its easier to comprehend
4.1000000 than 4.1427385. Unlocked grids always restrict precision to the minimum needed for a given
magnitude. This produces a friendly scale that makes it easier to determine the range between the
gridlines when data is formatted for display or printing.
With unlocked horizontal grids, the horizontal scale values printed on a graph may not match the
horizontal scale values displayed on the application screen. For example, horizontal scale values
Displayed in the application: 0.00000 7.50000 15.00000 22.50000
Printed: 0.00000 7.50125 15.00250 22.50375
The precision will only match when using the Visible area print option. With selected area or entire
graph options, the precision will not match when grids are unlocked because friendly grid scaling is
applied on screen, but is not used during printing where the range is fixed to fill the entire page.
Note that the Zoom tool and vertical autoscale may produce different results. To accommodate the grid
precision, the Zoom result may be slightly more than specified in the zoom box. For precise correlation
from selected area to result, lock the grids (horizontal and vertical). Precision is not restricted for locked
grids or display ranges manually entered in the axis setting dialogs.
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Journal Details
To create a journal, select the icon from the toolbar or choose File > New > Graph-Specific Journal or
Independent Journal. To toggle the graph-specific journal display, select the icon from the toolbar. Or
after opening a new journal, choose Edit > Journal > Show Journal.
Once a Journal is open, text and data can be entered. To enter text, just begin typing when the journal is open.
AcqKnowledge will automatically wrap the text to fit the screen width.
In addition to File and Edit menus, there are Time Stamp, Date Stamp and Auto Time
functions available in the journal window.
- Time and Date stamps refer to the computers clock to record the time and date, respectively, directly
into the Journal.
- Auto Time function records the time at the instant the carriage return is pressed, which is useful for
tagging commands as data is collected.
Measurements and data may also be pasted into an open Journal. To paste measurements into an open
Journal, select an area and choose Paste measurements from the Edit > Journal menu. Paste to Journal
functions only work if a Journal is open and vary for each journal type:
Graph-specific journals can only receive measurements and wave data from their associated graph
view
Independent Journals can receive measurements and wave data from any open graph. Results will be
put into both the graph-specific journal and the independent journal. Use Journal Preferences to auto-
paste to an independent journal if desired.
Set the Journal Preferences (page 425) to simultaneously record measurement name and units or control Event
(marker) paste functionality and detail.
To paste waveform data into a Journal, select an area and choose Paste Wave Data from the Edit >
Journal menu. Allow several seconds for the text file to be written. The result is a text file of your wave data
pasted into your active journal.
TIP: When pasting a graph into a Journal: Pressing the Ctrl key (PC) or the Alt key
(Mac) will launch a dialog allowing the image to be resized prior to pasting.
A useful feature of the Journal is that it works in connection with the Cycle/Peak Detector and other
measurement functions to paste in values from waveform data for further analysis.
In the example above, the peak-to-peak and delta t measurements were pasted from the open graph window to
the Journal. See the Journal paste section on page 261 for more information on how to paste information to
Journal files.
Use Save as/Open Journal Template to retain SOP text, or standardize lab/computer details for record
keeping.
Journal Contextual Menu
The Journal contextual menu allows quick access to common text
editing functions, as well as a tool for easily re-docking the Journal
window to any edge of the graph. To activate this menu, right-click
anywhere within the Journal window.

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Part A Getting Started 81
Rich Journals
The AcqKnowledge 4.2 Journal adds powerful rich text editing tools, offering advanced functionality
common to most word processing programs. The following toolbar options are available within the Journal
window:
- Font family
- Font style: bold, italic, underline
- Paragraph alignment: left, right, center, justify
- Font color
The following items can be pasted or embedded into the Journal text:
- Images
- Numbered lists
- Bulleted lists
- Tables
- Numerical statistics or expressions
Images must reside within a document in order to be pasted into the Journal. Pasting image files directly from
a location such as the Desktop is not currently supported.
Journal Toolbar Buttons
The Journal toolbar controls all formatting functions within the Journal window. Although the settings
customized in this toolbar are retained within a saved Journal, global default settings for subsequent Journals
are not overridden. To change the global defaults, the overall Journal Preference settings must be modified.
(Edit > Journal > Preferences). For more information, see Journal Preferences on page 425.

Journal Toolbar Icon Function Explanation

Clear Clears text from Journal window

Replace Replaces Journal text with contents of external text file

Save Saves selected or full Journal text to an external text file

Page Setup Opens dialog for modifying Journal text print configuration

Print Prints the Journal text to the default printer

Time stamp Inserts current time into Journal

Date stamp Inserts current date into Journal

Time AND Date Inserts current time and date into Journal when Enter/Return key is pressed
Font Use to select font type and size for Journal session

Text style Use to bold, italicize or underline text

Text alignment Aligns paragraph text to left, center, right or justified position

Font color Selects color of Journal text

Numbering Toggles text numbering on and off
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Bulleting Toggles text bulleting on and off

Increase indent Increases indent in a bulleted or numbered list*

Decrease indent Decreases indent in a bulleted or numbered list

Insert link Adds hyperlink to Journal

Table Inserts a table into the Journal

Table row Adds a row to the table **

Table column Adds a column to the table

Delete table row Removes selected row from the table

Delete table
column
Removes selected column from the table

Merge cells Merges selected cells within the table

Split cells Splits selected cells within the table
*Active only when cursor is positioned within a bulleted or numbered list.
**Additional table tools are active only when a table is present.
NOTE: If the AcqKnowledge graph or Journal windows are decreased in size, the Journal toolbar will
become truncated and some buttons may no longer be in view. Buttons no longer visible on the toolbar can be
found in drop-down menus indicated by arrows. (See below)

Journal Numerical Table Tools
The Numerical Table Tools function allows easy insertion of measurements and numerical data into a Journal
table, which can then be computed and evaluated via basic mathematical operations and expressions. This
eliminates the need to export data to a spreadsheet application in order to validate statistics gathered during
the course of an experiment.
Numerical Tools operations permitted within a Journal table:
Insert a single measurement value
Insert all measurement values
Insert all measurement values with header row
Sum, Mean and Standard Deviation statistics for table rows and columns
Expression evaluation
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Part A Getting Started 83

Menu Item Function
Undo Removes previous operation
Select All Selects all cell contents
Insert Single Measurement Value Pastes single selected measurement value into cell
Insert All Measurement Values Pastes all measurement values into cells
Row Statistics Performs Sum, Mean or Standard Deviation operations on row data
Column Statistics Performs Sum, Mean or Standard Deviation operations on column data
Evaluate Expression Performs mathematical operations and functions on cell contents
Word Wrap Wraps text within visible Journal area. (Does not apply to table cells)

Example of Sum, Mean or Standard
Sum, Mean or Standard Deviation operations can be easily performed on table data. Right clicking within a
cell opens a contextual menu containing available operations under Row or Column statistics. Choose an
operation, and the result will appear in the selected cell. (See sum example below)

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Example of Evaluate Expression
This feature works very much like Excel
.
Simply enter the cell identifiers into an empty cell, then right-click
and choose Evaluate Expression. The formula occupying the cell will be computed and be replaced by the
result. The mathematical operations and functions available for standard Biopac Expression syntaxes may be
used. (Transform > Expression). Expressions can be created beforehand then copied and pasted into a
Numerical Tools Table cell.
















If the expression syntax used is incorrect or invalid, a warning dialog will appear.


TIP: To correct a mistake, use the Ctrl+Z (PC) or Command+Z (Mac)
keystroke to restore the previous cell data. Multiple levels of undo are
supported.

Adding a hyperlink to the Journal
Use the Journal hyperlink toolbar button to insert a link to a web address into the Journal. This
operation is very similar to adding regular text.
1. Click into the Journal at the desired position for the link to appear.
2. Click on the Insert link toolbar button
3. Add the web address and some text identifying the link into the URL and Text fields.
NOTE: For the link to be active, the http:// designation must be entered before the web address.

4. Click OK, and the live link will appear in the Journal.
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Part A Getting Started 85

- To format the link text, select the link and use the Journal formatting tools.
- To edit the link text, position the cursor at the end of the link and use the arrow keys to
navigate to the desired portion. Backspace to remove unwanted text and type in new text.
- To delete a link, select the text and use the Delete key.
- Once a link has been created, the URL portion cannot be edited from within the Journal, nor
can the original Insert hyperlink dialog be recalled. If the URL itself needs to be edited, a
new link must be created using the Insert Link button.
Select a waveform / channel
Although multiple waveforms can be displayed, only
one waveform at a time is considered active. Most
software functions only apply to the active waveform,
which is also referred to as the selected channel.
Selecting a channel allows you to highlight all or part
of that waveform, and enables you to perform
transformations on a given channel.
In the upper left corner of the graph window there is a
series of numbered boxes that represent each channel of
data. The numbers in the boxes correspond to the
channel used to acquire the data (the specifics of setting
up channels are discussed on page 34). In the sample
file, ECG channels are represented by channels 1 and 2,
with respiration on channel 3 and blood pressure on
channel 4.
To select a channel, position the cursor over the channel box that
corresponds to the desired channel and click the mouse button or position the
cursor on the waveform of interest and click the mouse button.
Note that the selected channel box appears depressed and the channel label to
the right of the channel boxes changes to correspond to the selected channel.
Additionally, the channel label in the display (on the left edge of the track) will
be highlighted for the active channel.

Channel Labels
Each channel has a label on the left and right edge of the graph window.
The left label is used to identify the contents of each channel (ECG,
Respiration, etc.).
The right label is used to denote the units for each channels amplitude scale
(usually scaled in terms of Volts).


When a channel is active, its label is highlighted and also
appears by the channel boxes.
To change the label for a given channel
during or before acquisition
(including Append mode)
revise the MP150 menu > Set Up Channels label text
post-acquisition / analysis only
click the left label enter the desired text in the dialog

AcqKnowledge 4 Channel label
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Label and Units change prompts are separate. Click the left to
change the label and on the right (wrench icon in vertical scale)
to change the units. The label can be up to 40 characters.


Show/Hide Channel

You can hide a waveform display without
changing the data file. To hide a channel,
Windows: Alt+click in channel box.
Mac OS X: Option+click in channel box.
When a channel is hidden, the channel box will
have a slash through it. You may view a hidden
channel by holding down the Alt or Option key
and clicking in the channel box again. Channels 2
and 4 are hidden in the following display:


Focus Areas
Focus areas are comprised of selected time ranges within the graph. The purpose of the Focus on tool is to
easily isolate selected areas within the graph window for discrete analysis. This can be useful for identifying
areas of interest within a larger data set by highlighting, naming and storing them permanently in the graph.
When a focus area is assigned, that portion of the graph will appear shaded with borders appearing at the
edges. The assigned focus area label will be displayed vertically in the shaded area. (See following page for
example.) Focus areas may be defined via the Focus on toolbar above the graph, in the Output tab of the
Find Cycle Analysis feature, and once defined, can be selected within the setups for most Specialized
Analysis tools.
- Focus areas are graph level data, similar to events. Defining a focus area in one data view defines it
for all data views, etc.
- Focus areas are drawn only for graph windows in chart, stacked plot, or scope mode. They are
overlaid on top of data and events but underneath text annotations and selections.
- Focus areas may overlap.
- Each focus area is required to have a unique name.
Creating Focus Areas
To create a focus area:
1. Select an area of interest in the graph data using the I-beam tool or selection palette.
2. Create the focus area using one of the following methods:
- Click on the Add (+) button to the right of the Focus on toolbar.
- Choose Display > Create Focus Area.
- Right-clicking in the graph and choosing Create Focus Area from the contextual menu.
3. Name the focus area by typing into the label field.
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Part A Getting Started 87


The new focus area label will appear in the Focus on toolbar field.

The new focus area and label will appear in the graph.

Multiple and overlapping focus areas can be created by selecting additional data and using the Add (+)
button.
Navigate quickly to a focus area time selection in the horizontal axis by selecting its label from the
Focus on toolbar field.

To remove a focus area, use the minus Focus on toolbar button.
To rename a focus area, use the ellipses toolbar button.
Most Specialized Analysis tools can be limited to running analysis on a focus area by choosing the focus
areas only option in the setup dialog.

Focus areas can be included or excluded from a printed graph by selecting or deselecting the Print focus
areas option in Print Setup.
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Focus area preferences can be modified by using Display > Preferences > Focus Areas. For further details
see pages 422 and 426.
For Find Cycle focus area options, see the Find Cycle section on page 307.
To create focus areas in analysis mode based on events or appended segments, see the Specialized
Analysis > Focus Areas section on page 363.
Measurements
A convenient feature in AcqKnowledge is the popup measurement windows. A variety of
different measurements can be taken, and you can display different measurements from
the same channel and/or similar measurements from different waveforms. AcqKnowledge
can display measurements for the selected channel or for any other channel. By default,
AcqKnowledge displays measurements from the selected channel (as denoted by the
SC in the measurement boxes).
To select a channel for measurement, position the cursor over the part of the
measurement window that reads SC. Click the mouse button and choose a channel
number from the pull-down menu. The channel numbers in the pull-down menu
correspond to the numbers in the channel boxes in the upper left corner of the graph
window.
To select a measurement, position the cursor on a measurement box and click the mouse
button. Choose a measurement from the pull-down menu; see page 92 for measurement
functions and the minimum samples for each (some of the values are single point
measurements while others require at least two points to be selected).
The measurements in the upper half of the menu reflect amplitude measurements, or
measurements which contain information about the vertical (amplitude) scale. Other
measurements use information taken from the horizontal axis (usually) and are found on
the section of the pull-down menu below the dividing line. Some of the measurement
options change (or are disabled) if units are selected for the horizontal scale.

In some cases, the computations involved in the measurement can produce nonsensical
results (such as dividing by zero, or calculating a BPM from a single point). In those
cases, you may get a measurement value like INF or ****. This means that the result was
undefined at this point.
Measurement menus are tinted to match the color of the corresponding waveform.

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Part A Getting Started 89
Measurement Display

The number of measurement rows is set in Preferences > Measurements, as well as precision of units.



Measurement Area
It is important to remember that AcqKnowledge is always selecting either a single point or an area spanning
multiple sample points. If an area is defined and a single point measurement (such as Time) is selected, the
measurement will reflect the last selected point.

Single-point measurements
When a single point is selected, the cursor will blink. The following graph shows how the I-beam is
used to select a single point for measurements.


Selected range measurements
Drag the I-beam cursor to select an area; the selected area will be highlighted.
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IMPORTANT!
The first data point is plotted at zero (on the left edge of the graph); the first visible data point is sample
point 2. The selected areas below demonstrate this concept.


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Part A Getting Started 91


Measurements and Measurement Presets
Measurements are commonly used in conjunction with the cycle detector and other analysis protocols to
perform data reduction. In complex data analysis using the cycle detector, often multiple different sets of
measurements may be used to perform multiple extraction passes on the data. The measurement presets
feature allows users to create multiple predefined measurement configurations and apply them to the graph to
change between different configurations. All aspects of the measurement configuration are stored, including
measurement functions, any parameters for the measurement, source channel, and number of measurement
rows. For more details on this function, see MeasurementsToobar section on page 61.
Measurement Validation
You can validate measurements with the ValidateMeasurements.acq sample file included with the software.
Pay attention to the Sample data file section of the measurement definitions that begin on page 92, and
where included, note which sample points to use for validation (i.e., the first four sample points are used to
validate the Correlate measurement using the ValidateMeasurements.acq file).
Other sample files configured for specific measurement types include spreadsheets to provide external data
necessary for measurement verification. Each spreadsheet contains procedures and examples for the
associated measurement data file. These sample data files consist of Event Measurements.acq, Traditional.acq
(standard mathematical measurements included in AcqKnowledge,) Expression Sum_Calculate.acq and
Correl Coef.acq (Correlation Coefficient).
Measurement Info / Parameters
Measurements containing parameters have an i for
info button next to the measurement type in the measurement bar. Click the button to generate a dialog to edit
the parameters. To paste parameters, enable the Journal Preference via Display > Preferences > Journal >
Measurement paste settings > Include measurement parameters.
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Measurement Interpolation
On a down-sampled channel, the cursor can fall on a point between physical samples. In such cases, in the
Line Plot mode only, some measurements will display interpolated values; the value is obtained by linear
interpolation with respect to the two adjoining samples.
To disable measurement interpolation, uncheck the Use linear interpolation option in the Display >
Preferences dialog.
If interpolation is disabled for Line Plot, or any time Step Plot or Dot Plot is selected, measurements
take on the value of the first physical sample immediately to the left of the cursor or edge of the
selection.
When measurements are pasted to the Journal, there is no indication of interpolated measurements.
A Calculation measurement can be an interpolated value. When a measurement uses an interpolated
value, the result box background changes from gray to light purple.
The Delta S and Samples measurements are never interpolated.
Measurements will not be interpolated if all measurements are set to SC (selected channel); the
cursor will snap to the left for the measurements.
Measurement tooltips will reflect measurement interpolation.
Exporting measurements
One of the most important reasons to take measurements is to save them; AcqKnowledge allows you to store
and export these measurements in different formats.
Copying measurements to the journal:
To copy measurements (exactly as they appear in the measurement windows) and paste them to the
Journal, select Edit > Journal > Paste measurement. Under the default settings, only the values
themselves are copied to the journal; you can change the settings to include the measurement name and
other options under Display > Preferences > Journal
Copying measurements to the clipboard:
To copy measurements (exactly as they appear in the measurement windows) to the clipboard and paste
them into a word processor or other application, select Edit > Clipboard > Copy measurements. Under
the default settings, only the values themselves are copied to the clipboard; you can change the settings
to include the measurement name and other options via Display > Preferences > Journal.
Measurement Definitions
The table below explains the measurement options available and the range required for each. The default
option is for time to be displayed on the horizontal axis, although it can be set to display frequency or
arbitrary units (see page 410 for details on how to change the horizontal scaling options). Unless otherwise
noted, all of the measurements described here relate to those displayed when the horizontal scale reflects time.
Measurement Area Explanation
Area Minimum area:
3 samples

Uses:
All points of
selected area
Area computes the total area among the waveform and the straight line that is
drawn between the endpoints.
Area is expressed in terms of (amplitude units multiplied by horizontal units) and
calculated using the formula:
( ) ( ) ( ) ( ) ( )
2
1
1
1 1
i
n
i
i i i i
x
x y x f x y x f Area
A
- + =

=
+ +

Where:
nnumber of samples;
iindex (i = 1.n-1);
1
,
+ i i
x x
- values of two neighboring points at horizontal axis ( the first
point, the last point);
1
x
n
x
( ) ( )
1
,
+ i i
x f x f - values of two neighboring points of a curve (vertical axis);
( ) ( )
1
,
+ i i
x y x y - values of two neighboring points of a straight line (vertical axis).
At the endpoints y( )= f( ) and y( )= f( ).
1
x
1
x
n
x
n
x
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Part A Getting Started 93
Measurement Area Explanation
1
A
= A
n
X
x
i
- horizontal sample interval;
The value of a straight line can be found by formula:
( ) b x m x y
i i
+ - =
( )
1 1
x m x f b - = - intercept;
X
Y
m
A
A
=
- slope of the straight line;
( ) ( )
1
x f x f Y
n
= A - vertical distance of increase at vertical axis;
1
x x X
n
= A - horizontal distance of increase at horizontal axis.
Sample plot:

The area of the shaded portion is the result.
Note: The Area measurement is similar to the Integral measurement except that a
straight line is used (instead of zero) as the baseline for integration.











Results: This calculation will always return a positive result.
Units: Volts - sec.
Sample data file: ValidateMeasurements.ACQ
Result: 0.4533 Volts - sec.
BPM
(Time domain
only)
Minimum area:
2 samples

Uses:
BPM (beats per minute) computes the time difference between the first and last
points and extrapolates BPM by computing the reciprocal of this difference,
getting the absolute value of it and multiplying by 60 (60 sec).
The formula for calculation of BPM is:
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94 AcqKnowledge 4 Software Guide
Measurement Area Explanation
Endpoints of
selected area
60
1
1
-
|
|
.
|

\
|

=
x x
BPM
n

Where:
n
x x ,
1
- values of the horizontal axis at the endpoints of selected area.
Note: As mentioned, this measurement provides essentially the same information
as the Delta T and Freq measurement.
Results: Only a positive value.
Units: BPM.
Calculate Minimum area:
2 sources

Uses:
Results of
measurements
used in
calculation
Calculate can be used to perform a calculation using the other measurement
results. For example, you can divide the mean pressure by the mean flow.
When Calculate is selected, the channel selection box disappears.

The result box will read Off until a calculation is performed, and then it will
display the result of the calculation. As you change the selected area, the
calculation will update automatically.
To perform a calculation, generate the Waveform Arithmetic dialog via
Ctrl-Click or right mouse click the Calculate measurement type box or click the
info button next to the measurement type box .


Use the pull-down menus to select Sources and Operand.
Measurements are listed by their position in the measurement display grid (i.e.,
the top left measurement is Row A: Col 1). Only active, available channels appear
lculation is
be
and it
ox.
in the Source menu.

Calculation measurement Source operands are updated before a Ca
performed, which means that Calculations can be based on measurements that
are located after them in the measurement row/column ordering.
ulation measurements ca Calc n include other Calculation measurements as their
operands.
- If a cyclic dependency is introduced, the result reads Error.
- When interpolation is being used, a Calculation measurement can also
an interpolated value.
- If either of the operands of a Calculation is interpolated, the result will be
displayed as an interpolated value (with a light purple background).
The Operand pull-down menu includes: Addition, Subtraction, Multiplication,
Division, Exponential.
ect Source: K, constant The Constant entry box is activated when you sel
allows you to define the constant value to be used in the calculation.
To add units to the calculation result, select the Units entry box and define the
units abbreviation.
Click OK to see the calculation result in the calculation measurement b
Cap_Dim Capacity Dimension; fractal dimension estimate.
(Fractals measure the amount of self-similarity in a data set. AcqKnowledge
offers three alternate estimates for fractal dimension: Cap_Dim, Corr_Dim, and
Inf_Dim. The estimates will not agree, based on the heuristic and the
parameters.)
Corr_Dim at estim Correl ion Dimension; fractal dimension ate. Always greater than capacity if
parameters are the same. (See fractals note at Cap_Dim.)
Correlate Minimum area:
2 samples

Uses:
All points of
sel t of a lin w data
set and
Co es the Pearson produc icient, r, over the rrelate provid t moment correlation coeff
ea o ected area and reflects the exten r relationship between t
s: x - values of horizontal axis
i
( ) - values of a curve (
i
two ranges of data mov
x f vertical axis).
e together. You can use Correlate to determine whether
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Part A Getting Started 95
Measurement Area Explanation
selected area Association Correlation
Large values with large values Positive correlation
with large values Negative correlation
Correlation near zero
The formula for the correlation coefficient is:
Correlate =
Small values
Unrelated
( ) ( ) ( )
( ) ( ) ( ) ( )
(
(

|
.
|

\
|
- -
(
(

=1 i
n

|
.
|

\
|

|
.
|

\
|
- |
.
|

\
|
- -


= = =
= = =
2
1 1
2
2
1
2
1 1 1
n
i
i
n
i
i
n
i
i
n
i
n
i
n
i
i
n
i
i i i
x f x f n x x
x f x x f x n



Where:
nnumber of samples;
of points at horizontal axis ( the first point, the last point);
iindex (i = 1..n);
x
i
x values
1

n
x
( ) x f - values of
i
po
Results:
ints of a curve ( vertical axis).

eturns a dimensionless index that ranges from -1.0 to 1.0 inclusive. R
Units: None
Sample data file: ValidateMeasurements.ACQ
Result: -0.74825(for whole wave) and 0.95917 (for first four
sample points).

Delta Minimum area:
2 samples

Uses:
Endpoints of
selected area
Delta returns th ints of the
Delta
e difference between the amplitude values at the endpo
selected area.
( ) (
1
x f x f
n
) =

Where:
( )
1
x f , ( )
n
x f values of a curve at the endpoints of selected area.


Results:
If e starting location is greater than the data value at the
cursor, then a negative delta will result. Otherwise, a
ult.
the data value at th
ending location of the
positive delta will res
Units: Volts
Sample data file: ValidateMeasurements.ACQ
esult shows the
absolute value of change of amplitude (2) and the minus
sign means a decrease of amplitude.
Result: -2 Volts (for whole wave). This r
Delta S Minimum area:
1 sample

Uses:
nts of
Delta S returns the difference in sample points between the end and beginning of
Endpoi
selected area
the selected area.
Results: This calculation will always return a positive result.
Units: Samples

Delta T(time)
Delta F
(frequency)
Delta X (arbitrary
unit)
Minimum area:
2 samples

Uses:
Endpoints of
selected area
The Delta T/F/X measurem ws the relative distance in horizontal units
bet endpoints of th nly one of these three units will be
dis the pop-up me by the horizontal
Measurement
ent sho
ween the e selected area. O
played in nu at a given time, as determined
scale settings.
Hori tal Axis zon
Delta T
F Frequency (FFT)
Del
The fo
Time
Delta
ta X Arbitrary units (Histogram Bins)
rmula for Delta T/F/X is:
Delta T
1
x x
n
=

Where:
x
n
x , - values of horizontal axis at the endpoints of selected area.
1
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96 AcqKnowledge 4 Software Guide
Measurement Area Explanation
Results:
If the data value at the starting location is greater than the data value at the
ion of the c ending locat
positive delta will result.
For Delta T measurem
ursor, then a negative delta will result. Otherwise, a
ents with the horizontal axis format set to HH:MM:SS.
cimal
eater than 60 seconds, you will see an HH:MM:SS
(See page 71 for tal scaling).
nits
- For values less than 60 seconds, you will get a value in de
seconds.
- For values gr
format value
details on how to change the horizon
U :
Delta T: Seconds (sec.) Delta X: arbitrary unit
Delta F: Hz
Sample data file: ValidateMeasurements.ACQ
Result: 0.12 sec. (for whole wave).

Evt_amp
unitless. Specify Type, Location, and Extract;
h may be
different from the channel on which events are defined.
Extracts the value of the measurement channel at the times where events are
defined. The measurement result is
see page 214 for details.
The amplitude is always taken from the measurement channel, whic
Evt_amp can be useful for extracting information such as the average T wave
height within the selected interval.
Evt_count s the number of events within the selected area. The measurement Evaluate
result is unitless. Specify Type and Location; see page 215 for details.

Evt_loc e
ation, and Extract; see page 215 for
Extracts information about the times of events. The measurement result uses th
units of the horizontal axis. Specify Type, Loc
details.
Expression

ta
de, the first step in evaluation searches through the
ose
the
sample. It is evaluated at the waveform sampling rate
al expression becomes the value of the
measurement.
Generates the Expression transformation dialog (page 136) and offers Source
MC Measurement Channel instead of SC Selected Channel to build recursive
formulas, i.e. result of the expression as it was evaluated x samples ago. Da
within the selected area is not changed.
Evaluation rules:
When a new selection is ma
measurement expression for any MMT() invocations. Any measurement wh
value is needed by MMT () is computed at this time prior to the expression
evaluation. This behavior is similar to calculation channels and successfully
allows measurements to the right and bottom of the expression measurement to
be used in the expression.
The expression is subsequently evaluated from the leftmost sample in
selection to the right most
of its source channel. Interpolation is not used at the boundaries to maintain a
consistent sample interval for the expression. After each expression evaluation,
emory for potential negative MC result references. the result is cached in m
The rightmost value of the fin
F
d

req (time
omain only)
It is important
to note
the
f the

spectral
analysis, use
the FFT
function (see
page 300).
This does not
compute
frequency
spectra o
data.
To perform a
Minimum area:
2 samples

Uses:
Endpoints of
selected area
Freq computes the frequency etween the en points of the selected area
by computing the reciprocal of the absolute value of time difference in that area.
ula for Freq is:
in Hz b d
The form
Freq
|
|
.

\

=
1
x x
n

Where:
| |
1

rea.
n
x x ,
1
- values of horizontal axis at the endpoints of selected a
The information provided by this measurement is directly related to the Delta T
and BPM measurements, and is related to a lesser extent to Delta S
measurement. That is, if the Delta T interval between two adjacent peaks is
calculated, the BPM and Freq measurement can be extrapolated.
If the sampling rate is known, the Delta S can also be derived.
In the following example, you can see Delta T, Freq and BPM measurements for
the particular area. The Delta S can also be derived.
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Part A Getting Started 97
Measurement Area Explanation

Selected area with measurements that describe
the same interval in different terms.

Note: It is important to note that this does not compute the frequency spectra of
the data. To perform a spectra analysis, use the FFT function (described on page
300).
Freq (or frequency) is only available in time domain windows.
Results: This calculation will always return a positive result.
Units: Hz
Sample data file: ValidateMeasurements.ACQ
Result: 8.33 Hz (for whole wave).
Inf_Dim Information Dimension; fractal dimension estimate. (See fractals note at
Cap_Dim.)
Integral Minimum area:
2 samples

Uses:
All points of
selected area
Integral computes the integral value of the data samples between the endpoints
of the selected area. This is essentially a running summation of the data.
Integral is expressed in terms of (amplitude units multiplied by horizontal units)
and calculated using the following formula.
Integral =
( ) ( ) | |
2
1
1
1
i
n
i
i i
x
x f x f
A
- +

=
+
Where:
nnumber of samples;
iindex (i = 1.n-1);
1
,
+ i i
x x
- values of two neighboring points at horizontal axis ( the first
point, the last point);
1
x
n
x
( ) ( )
1
,
+ i i
x f x f - values of two neighboring points of a curve (vertical axis);
1
A
= A
n
X
x
i
- horizontal sample interval;
1
x x X
n
= A - horizontal distance of increase at horizontal axis.
The following plot graphically represents the Integral calculation.
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98 AcqKnowledge 4 Software Guide
Measurement Area Explanation

The area of the shaded portion is the result.
Results: The Integral calculation can return a negative value if the selected area
of the waveform extends below zero.
Units: Voltssec.
Sample data file: ValidateMeasurements.ACQ
Result: 0.300 Volts -sec.(for first 6 sample points) and
0.155 Volts -sec.(for last 6 sample pointsthe wave below
zero).
Kurtosis Kurtosis indicates the degree of peakedness in a distribution, e.g. the size of the
tails of the distribution. Distributions that have sharp peaks in their center have
positive kurtosis; flatter distributions have negative kurtosis. A normal distribution
has a kurtosis of 0. The following formula is used to extract kurtosis
( )
( )
2
2
1
4
1
|
|
|
|
|
.
|

\
|

=
=
n
x x
n
x x
kurtosis
n
i
i
n
i
i

Where from a signal (x) containing n points:
Lin_reg Minimum area:
2 samples

Uses:
All points of
selected area
Linear regression is a better method to calculate the slope when you have noisy,
erratic data.
For advanced modeling options, see Nonlinear modeling on page 297.
Lin_reg computes the non-standard regression coefficient, which describes the
unit change in f (x) (vertical axis values) per unit change in x (horizontal axis).
For the selected area, Lin_reg computes the linear regression of the line drawn
as a best fit for all selected data points using the following formula:
Lin_reg =
( ) ( ) (
( )
)


= =
= = =
|
.
|

\
|
-
|
.
|

\
|
- |
.
|

\
|
- -
n
i
n
i
i i
n
i
n
i
i
n
i
i i i
x x n
x f x x f x n
1
2
1
2
1 1 1

Where:
nnumber of samples;
iindex (i = 1.n);
i
x values of points at horizontal axis ( the first point, the last point);
1
x
n
x
( )
i
x f - values of points of a curve ( vertical axis).
Note: For a single point, Lin_reg computes the linear regression of the line drawn
between the two samples on either side of the cursor.
Results:
If the data value at the starting location is greater than the data value at the
ending location of the cursor, then a negative delta will result. Otherwise, a
positive delta will result.
Units: Volts/sec.
This value is normally expressed in unit change per second (time rather then
samples points) since high sampling rates can artificially deflate the value of the
slope. If the horizontal axis is set to display Frequency or Arbitrary units, the slope
will be expressed as unit change in corresponding vertical axis values (frequency
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Part A Getting Started 99
Measurement Area Explanation
or arbitrary units, respectively).
Sample data file: ValidateMeasurements.ACQ
Result: 230.00 Volts/sec. (for 1-4 samples) and
170.00 Volts/sec. (for samples 4-7).
Lyapunov Lyapunov exponent describes the exponential rate of divergence of a system
when perturbed from its initial conditions. For instance, if the system is started
from two slightly different locations, this indicates how different their results will be
with time. Stable experiments have exponents equal to zero. Specify an
embedding dimension and a time delay; produces a single-valued measure. This
measure is quite dependent on the amount of data used.
Max Minimum area:
1 sample

Uses:
All points of
selected area
Max (maximum) shows the maximum amplitude value of the data samples
between the endpoints of the selected area. To compare peak heights, select
each peakyou can easily see the maximum peak values or paste the results to
the journal. Also, since you can simultaneously obtain measurements for different
channels, you can easily compare maximum values for different channels.
Note: For a single point, Max shows the amplitude value in this point.
Units: Volts
Max T Minimum area:
1 sample

Uses:
All points of
selected area
Max T shows the time of the data point that represents the maximum value of the
data samples between the endpoints of the selected area.
Note: For a single point, Max T shows the time value in this point.
Units: Seconds
Mean Minimum area:
2 samples

Uses:
All points of
selected area
Mean computes the mean amplitude value of the data samples between the
endpoints of the selected area, according to the formula:
Mean =
( )

=
-
n
i
i
x f
n
1
1

Where:
nnumber of samples;
iindex (i = 1.n);
i
x values of points at horizontal axis; ( the first point, the last point);
1
x
n
x
( )
i
x f - values of points of a curve ( vertical axis).

Units: Volts
Sample data file: ValidateMeasurements.ACQ
Result: 1.538462 Volts (for whole wave).
Median Minimum area:
2 samples

Uses:
All points of
selected area
Median shows the median value from the selected area.
Note: The median and calculation is processor-intensive and can take a long
time, so you should only select this measurement option when you are actually
ready to calculate. Until then, set the measurement to none.
Units: Volts
Median T Minimum area:
2 samples

Uses:
All points of
selected area
Median T shows the time of the data point that represents the median value of the
selected area.
Note: The median and calculation is processor-intensive and can take a long
time, so you should only select this measurement option when you are actually
ready to calculate. Until then, set the measurement to none.
Units: Seconds.





Min Minimum area:
1 sample

Uses:
All points of
selected area
Min (minimum) shows the minimum amplitude value of the data samples between
the endpoints of the selected area.
Note: For a single point, Min shows the amplitude value in this point.
Units: Volts.
Min T Minimum area:
1 sample

Uses:
All points of
Min T shows the time of the data point that represent the minimum value of the
data samples between the endpoints of the selected area.
Note: For a single point, Min T shows the time value in this point.
Units: Seconds.

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100 AcqKnowledge 4 Software Guide
Measurement Area Explanation
selected area
Moment

Uses:
All points of
selected area
Central Moment is a general-purpose statistical computation that can be used to
compute central variance and other higher-order moments of the data within the
selected area. Specify the order as an integer (generally). The central moment is
computed using the following formula:
( )
n
x x
m
n
i
i
m

=

=
1

Where:
xsignal;
npoints;
morder.
Mut_inf Mutual Information determines how much could probabilistically be known about
an unknown signal given a known variable. Specify a time delay. Produces a
single valued result.
NLM Nonlinear modeling (also called arbitrary curve fitting) determines the best fit
model for the selected data of the selected channel. The measurement result
corresponds to the value of one of the parameters of the best fit. NLM can be
used to extract Tau (time delay LVP constant) for assessing cardiac condition.
See page 297 for nonlinear modeling details.
If a Model Expression uses MMT() syntax to reference a measurement and
that referenced measurement is linearly interpolated, the results of the NLM
measurement will also be displayed as being linearly interpolated.
When combined with the Cycle/Peak Detector (on page 307), the NLM
measurement can be useful for extracting cycle-by-cycle best fit models for
an entire waveform.
None n/a None does not produce a measurement value. Its useful if you are copying a
measurement to the clipboard or journal with a window size such that several
measurements are shown and you dont want them all copied.
P-P Minimum area:
2 samples

Uses:
All points of
selected area
P-P (peak-to-peak) shows the difference between the maximum amplitude value
and the minimum amplitude in the selected area.
Results: The result is always a positive value or zero.
Units: Volts
Sample data file: ValidateMeasurements.ACQ
Result: 13 Volts (for whole wave).
Samples Minimum area:
1 sample

Uses:
All points of
selected area
Samples shows the exact sample number of the selected waveform at the cursor
positionthe first data point is not displayed, but is plotted at zero.
See page 90 for examples of selected area Samples.
Note: When an area is selected, the measurement will indicate the sample
number at the last position of the cursor.
Units: Samples.
Skew Skew is a statistical measure of the degree of asymmetry in a distribution (away
from normal Gaussian distribution), e.g. if the distribution is weighted evenly or
trends toward an edge.
- A normal distribution has a skew of 0.
- A distribution with a prominent left tail has a negative skew.
- A distribution with a prominent right tail has a positive skew
The following formula is used to extract skew:
( )
( )
3
1
2
3
1
|
|
|
|
|
.
|

\
|

=
=
n
x x
n
x x
skew
n
i
i
n
i
i

Where a signal (x) contains n points:
Slope Minimum area:
2 samples



Slope computes the non-standard regression coefficient, which describes the unit
change in f (x) (vertical axis values) per unit change in x (horizontal axis).
For the selected area, Slope computes the slope of the straight line that intersects
the endpoints of the selected area, using the formula:
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Part A Getting Started 101
AcqKnowledge 4 Software Guide
Measurement Area Explanation
Uses:
All points of
selected area
Slope =
( ) ( )
1
1
x x
x f x f
n
n


Where:
( )
1
x f , ( )
n
x f values of a curve at the endpoints of selected area.
1
x , - values of horizontal axis at the endpoints of selected area.
n
x
This value is normally expressed in unit change per second (time rather then
samples points) since high sampling rates can artificially deflate the value of the
slope.
Note: Lin_reg (linear regression) is a better method to calculate the slope when
you have noisy, erratic data.
For a single point, Slope computes the slope of the line drawn between the two
samples: the selected sample point and the sample point to its left.
Results:
If the data value at the starting location is greater than the data value at the
ending location of the cursor, a negative delta will result. Otherwise, a positive
delta will result.
Units: Volts/sec. (or corresponding to Freq or Arbitrary setting)
Sample data file: ValidateMeasurements.ACQ
Result: 233.33333 Volts/sec. (for samples 1-4)
-166.66667 Volts/sec. (for samples 4-7) and
-16. 66667 Volts/sec. (for whole wave).

Stddev Minimum area:
2 samples

Uses:
All points of
selected area
Stddev computes the standard deviation value of the data samples between the
endpoints of the selected area. Variance estimates can be calculated by squaring
the standard deviation value.
The formula used to compute standard deviation is:
Stddev = ( )

|
.
|

\
|
-

n
i
i
f x f
n
1
2
1
1

Where:
nnumber of samples;
iindex (i = 1.n);
i
x values of points at horizontal axis ( the first point, the last point);
1
x
n
x
( )
i
x f - values of points of a curve ( vertical axis);

= f

( )

=
-
n
i
i
x f
n
1
1
- the mean amplitude value of the data samples between
the endpoints of the selected area.
Results: The result is always a positive value or zero.
Units: Volts
Sample data file: ValidateMeasurements.ACQ
Result: 3.09570 Volts (for samples 1-4),
1.000 Volts (for samples 10-12).


Sum Minimum area:
2 samples

Uses:
All points of
selected area
Sum extracts a mathematical sum of the amplitudes of all of the samples within
the selected area. This straight sum can be used as a building block for more
complicated formulas. Examples of its utility include HRV measurements, various
statistical measurements, and simple criteria for clustering. Sum is available from
within the measurement popup menus and from analysis scripts that allow for
extraction of measurements.
Time Minimum area:
1 samples

Uses:
All points of
selected area
See the X-axis: T measurement for explanation.
Value Minimum area:
1 sample

Value shows the exact amplitude value of the waveform at the cursor position.
For the selected area, Value indicates the value at the last position of the cursor,
corresponding to the direction the cursor was moved (the value will be the left-
102 AcqKnowledge 4 Software Guide
Measurement Area Explanation
Uses:
All points of
selected area
most sample point if the cursor was moved from right to left).
Units: Volts
X-axis:T/F/X
(horizontal units)
Minimum area:
1 sample

Uses:
All points of
selected area
The X-axis measurement is the exact value of the selected waveform at the
cursor position, based on the Horizontal Axis setting:
Measurement Horizontal Axis Setting Units
X-axis: T Time Sec.
X-axis: F Frequency Hz.
X-axis: X Arbitrary units Arb. units
For X-axis: T measurements, the time value is relative to the absolute time offset,
which is the time of the first sample point.
The X-axis: F measurement applies to frequency domain windows only (such as
FFT of frequency response plots). The Freq function for time domain windows is
described on page 96.
Note: If a range of values is selected; the measurement will indicate the horizontal
value at the last position of the cursor.
Results: This calculation will always return a positive result.

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103

Part BAcquisition Functions: The MP menu
Overview
The AcqKnowledge software adds acquisition and control capability to the complete MP System (MP150 or
MP36R). This section describes the commands and procedures used to establish the various acquisition
parameters for the MP System (MP150 or MP36R), including how to:
- Set Up channels for data acquisitions
- Control acquisition parameters such as sampling rate and duration
- Perform online calculations and digital filters
- Set acquisitions to begin on command from a mouse click or external trigger
- Display values numerically and graphically during an acquisition
- Output waveforms and digital signals during an acquisition
- Control the on-screen waveform display characteristics
Some of the basic functions involved in setting up an acquisition were covered in Part AGetting Started, but
this section will cover them in more detail, as well as describe some additional features. All the commands
covered here can be found under the MP150 menu.


104 AcqKnowledge 4 Software Guide
Acquisitions
Acquisition is defined as data collection from an external source (such as electrodes connected to an amplifier).
Before you begin an acquisition, make sure the MP data acquisition unit is turned on and connected to
your computer. Please refer to the BIOPAC Hardware Guide for more information on connections.
To begin collecting data and display data as it is being collected:
1. Launch the AcqKnowledge application (you can double click the AcqKnowledge icon).
2. Choose File > New and select document type Graph Window :



NOTE: If more than one hardware type has
been previously added via the Connect to
menu, these will also appear in the Choose
Type dialog (left).For deatails on connecting
additional hardware types, see page 155.
3. Set up the specific channels you want to acquire before starting the acquisition.
- See the Set Up Channels chapter (page 105 ) for details.
4. Set up the acquisition parameters (such as sampling rate, acquisition length, and data storage options.
- See the Set Up Acquisition chapter (page 151) for details.
Edit menu functionality during acquisition
The following Edit menu functions may move or alter memory and cannot be performed during acquisition:
Undo, Cut, Clear, Clear All, Paste, Insert Waveform, Duplicate waveform, and Remove Waveform.
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Part C Analysis Functions 105
Chapter 5 Set Up Channels
Set Up ChannelsThe Basics
Before you collect data, you need to specify how many channels you will be collecting data on, and at what rate
data is to be collected. Both of these functions are accomplished through menu items and dialogues. To enable
collection on a given channel, select Set Up Channels from the MP150 menu.
AcqKnowledge 4.1 offers two methods of analog channel setup:
New! Module-based setup View by Channels see page 107 for details


If using AcqKnowledge with BioHarness or B-Alert

, Analog channels can be turned


on/off but not changed.
Module-based analog channel setup
For MP150 units, AcqKnowledge 4.1 and higher introduces a module-oriented analog
channel setup option. In module mode, setup prompts the user to add modules/transducers
and establish parameters, plus it detects potential channel conflicts between software
assignment and the module channel switch setting and scales the signal to the correct value
and units.
The new module setup is recommended for easier setup and automatic scaling. In module mode, setup prompts
the user to add individual modules based upon the module number. For modules with transducers, the unique
transducers are added. The user is then prompted to input the settings of all of the switches on the modules and
then perform any calibration steps, if required. Using this information, the module setup automatically sets the
scaling and initial visual range to match the physical input units from the module or transducer. Additionally,
module-based setup detects potential channel conflicts between software channel assignment and module
channel assignment (red switch position).

1. From MP150 > Setup Channels, select the analog tab and click View by Modules...

2. Click Add New Module from the bottom of the dialog.

3. Select a module and click Add.

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4. If prompted, select a transducer and click Add.

5. Input the settings of the switch on the selected module and click OK. Set
the choose channel switch to the number set on the amplifier (some
amplifiers, such as the OXY100C, have a switch on the front of the
module).
Setup detects any potential channel conflicts between software
assignment and the modules red channel switch position.
6. Establish the configuration parameters (gain and filters) and click OK. It
is important to set the Gain and Filter settings to correspond to the switch
settings on the amplifier. The software uses this information to scale the
signal to the correct units. If the Gain is not set to match, the signal will
be scaled incorrectly.

7. Perform calibration steps, if required. The software will automatically
scale certain signals, if they only require a zero setting. However, some
signals require a two-point calibration. In this case, the software will
generate additional prompts for the scale values.

The following examples show the dialogs for setting up a force
transducer.
a. The software prompts the user for pretension amount; enter 0 if
pretension is not required.

b. Enter a low calibration value or 0 if calibrating between zero and a second weight, when OK is
clicked, he software will take a voltage reading.

c. Enter a high calibration value and click OK for the software will take a voltage reading.

Note When recording is started, the data may show an offset. This offset is the amount that was
entered in the pretension dialog. Adjust the tension applied to the transducer to center the signal
on zero.
Using this information, the module setup automatically sets the scaling and initial visual range to match
the physical input units from the module or transducer.
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Part C Analysis Functions 107
View by Channels
Channel Type
To specify the channel typeAnalog, Digital, or Calculationclick its tab at the top of the dialog.

For each channel you wish to collect data on, there are three options for channel setup: acquire, plot, and values.
These options appear as boxes on the left side of the Input Channels dialog.

Acquire
The first option is whether or not you wish to collect data on that channel. The default setup is not set to acquire
any channels. To collect data, position the cursor over the Acquire box (on the far left) and click the left mouse
button.
To leave hardware connected to the data acquisition unit, but have the software essentially ignore the channel,
leave the acquire box unchecked. For example, if an input device (such as an ECG100C amplifier) is set to
channel 7, data from that channel will not be collected unless the Acquire box is checked.

Plot
The second option is for plotting data. You will need to specify a Plot option for each channel. The Plot option
determines whether or not data will be plotted on the screen for each channel. Checking this option instructs the
software to plot data on your computers screen.
When this box is left unchecked, data will still be collected (assuming the Acquire box is checked) but it will
not be displayed during the acquisition.
In most cases, you will want to check this option. However, in large-scale acquisitions (i.e., many channels
and/or high sampling rates) you may want to uncheck this option for some channels to allow for faster display
rates or to increase the display area for important channels (see Appendix BHints for working with large
files). Alternatively, use a separate data view and enable channels for as desired for optimum viewing.
The Plot state is applied only on initial acquisition into a graph or template. If data has been previously
acquired, use the channel buttons in the graph window to change channel visibility.

Values
The third option enables incoming data values to be displayed either numerically and/or in a bar chart format
in a separate window during an acquisition. Checking this option allows you to open a window (by selecting
Show Input Values... under the MP150 menu) that displays the numeric value for each input with the Values
option checked. This option is especially useful for tracking slowly changing values such as heart rate,
respiration rate, or concentrations of chemicals in a substance. For more information on how input values are
displayed, please turn to page 218.

Channel
Click in the channel number box (i.e. A1) to make that channel active (selected) so its settings can be
established or edited.

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Label
You may attach an editable label to each channel. These labels allow you to provide a brief name for each
channel. To change the label for any channel, position the cursor in the area to the right of the channel numbers
(A1 through A16) under the label heading and enter a text label. You may key up to 38 characters and these
labels will appear next to the channel label boxes in the graph window. To edit the label after setup, use the Set
Up Channel dialog at any time, or right-click the active channel label in the graph window to generate the
Assign Channel Label dialog.

Presets
Calculation Presets are like templates for calculation channels. Each Preset stores:
a) Calculation channel type
b) parameters for that Calculation
c) channel-specific scaling
d) channel-specific sampling rate
e) channel name.
Calculation Presets establish settings to target application-specific analysis. Presets exist for a broad range of
analysis functions, including Fourier Linear Combiners and Adaptive Filtering. Start with existing presets for a
specific species or protocolfor example, human vs. small animal, or stationary vs. exercising measurements.
The Channel Setup dialog contains a Preset pop-up menu by each channel that lists the current Preset or, if no
Preset has been selected for that channel, the Calculation type (Integrate, Difference, etc.). When you select a
Preset for a particular channel, the channel is configured with the settings associated with that Preset.
The Setup dialog has a Presets pop-up menu that contains all of the Presets for the Calculation type being
configured. For instance, if a Difference Calculation channel is being configured, all Presets for the Difference
Calculation will be listed. Just click the Presets head and scroll to select the desired preset.

Calculation Presets
When you select a Preset, the Setup dialog is updated with the corresponding information.
The Setup dialog reads none if the channel configuration doesnt match any Preset. The menu will
flip to none when the settings for a channel are changed such that they no longer match a Preset.
You can create a new Preset from existing Calculation channels. Click Setup to display the
Calculation Setup dialog and click the New Preset button. The settings will be applied to the current
channel, and you will be prompted to enter a name for the new Preset. You cannot duplicate a Preset
name, which also means that you cannot use the default name of a Calculation channel type (Integrate,
Difference, etc.). The new Preset will be included in the pop-up menus and saved with the file.
To reorder channel Presets (by type, use, etc.), choose MP > Organize Channel Presets and then use the
up/down buttons as appropriate (see page 231).
Presets are not applicable to and therefore not selectable on Analog or Digital channels.

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Part C Analysis Functions 109
Channel Sampling Rate
The Variable Sampling Rate feature allows different channels of data to be down-sampled from the acquisition
sampling rate; calculation channel must use sampling rate less than or equal to the source channel. Choosing
lower sampling rates for signals where meaningful data falls below the Nyquist frequency of the acquisition
sampling rate allows more data to be stored in memory or on disk.
Offline operations that involve multiple channels must use the same sampling rate for all Source and
Destination channels. These operations include waveform editing, Waveform math, Expression
calculations and Template functions; notable exceptions are Off-line Averaging under Find Cycle/Peak
and Reset via a Control Channel under Integrate.
When wave data is copied to the clipboard or journal, data values will be inserted at the highest sampling
rate (channels with a lower sampling rate will snap to the left).
To set an arbitrary channel sample rate for analysis, use Transform > Resample (see page 291).
There is no restriction on the acquisition length when using Variable Sampling Rates.
When Variable Sampling Rates are used in conjunction with the Append mode, and the mode is started
and stopped manually, it is statistically possible that, prior to the next pass of the Append, extra data
points may be inserted in various data channels to line up the data (see sample on page 109). These
extra data points simply replicate the last sample in any affected channel.
To minimize the impact of the extra data points:
a) Make sure the lowest sampling rate is on the order of 10 Hz or higher, or
b) Dont use Variable Sampling Rates.




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Set Up ChannelsAdvanced
The previous section covered the basic options used in almost all acquisitions. In addition to the features
described above, a number of other options are available in terms of setting up channels. These advanced
features are also found under the Set Up Channels menu item.
Most acquisitions involve collecting analog signals and then displaying them on screen. It is frequently useful,
however, to collect other types of data (digital data, for instance) or to perform transformations on analog data
as it is being acquired. Channels containing digital signals and transformed analog signals can be collected in
addition to the 16 analog channels.
In the upper right hand corner of the Set Up Channels dialog, you will see the words Analog, Digital, and Calc.
These refer to (respectively) analog channels, digital channels, and Calculation channels. The general features
(acquiring, plotting, and the like) are the same for each type of channel, although there are considerable
differences between the type of data each channel is designed to handle. You may acquire up to 16 channels
each of analog, digital, and Calculation channels. Analog and digital channels may be acquired in any
combination, and the only requirement for Calculation channels is that you have at least one input channel
(either analog or digital).
Analog channels
Analog channels are the most common type of acquired channel and should be used to acquire any data with
continuous values. Examples of this include nearly all physiological applications where input devices
(transducers and electrodes) produce a continuous stream of varying data. The range of values for analog
channels is 10 Volts.
AcqKnowledge also allows you to rescale the signal on analog channels to more meaningful numbers. As an
example, imagine a temperature transducer is connected to an SKT100C amplifier with a gain setting of
5/Volt, and output set to channel 1. Ordinarily, the values from the amplifier would be read in as Volts or
milliVolts. For this acquisition, you need to express the signal from the transducer in terms of degrees
Fahrenheit. To calibrate the transducer, bring it to two known temperatures. At the first temperature, take a
voltage reading by selecting Show input values from the MP menu (see page 218 for a description of the Show
Input Values options). At 90 F, you will get a reading of 0 Volts. The transducer is then brought to a
temperature of 95 F, and you will get a reading of +1 Volts.
To scale the incoming signal to degrees F, click the Setup button in the Input Channels dialog.

Scaling dialog set to rescale Volts to degrees Fahrenheit and Use Mean Value Settings dialog
The Input Volts and Map (Scale) Value boxes reflect the value of the incoming signal and how it will be plotted
on the screen, respectively. Thus, an incoming signal of +1 Volts would be plotted as 95 F, whereas a signal of
0 Volts would be plotted as 90 F. AcqKnowledge will perform linear extrapolation for signal levels falling
outside this range (i.e., -2 Volts will be scaled to 80 F), as well as perform similar interpolation for values
between this range. Enter these numbers in the scaling dialog, type in degrees F for Units, and click OK.
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Part C Analysis Functions 111
As a shortcut for scaling channels, use the Cal 1 and Cal 2 buttons. Click either of these buttons to read in the
current voltage for the selected channel. In the above example, the transducer could simply be set to a known
temperature, then Cal 1 could be clicked, and then the temperature could be entered in the Map (Scale) value
box for Cal 1.
Next the transducer could be brought to another known temperature that is considerably higher or lower than
the first and click Cal 2 and the new known temperature could then be enter in the Map (Scale) value box for
Cal 2. AcqKnowledge calculates the slope and offset from the two points entered. Each data sample from
channel 1 will now be scaled according to the slope and offset calculations previously made. When an
acquisition is performed, the amplitude scale (vertical axis) will reflect the rescaled units.
It is important to note that Cal 1 and Cal 2 cannot be used when data is being acquired. In other
words, a channel must be calibrated before it can be acquired. To set the calibration for a given
channel, connect the input device to the MP data acquisition unit and power up the MP System
(MP150 or MP36R), and then perform your calibration before starting data acquisition.
The Calibrate all channels at the same time option is used when identical types of transducers or signals are
being simultaneously recorded on two or more channels.
If this option is selected, when Cal 1 or Cal 2 is pressed:
- Map (Scale) Value will be updated for all active channels
- Input Volts need to be updated for each channel individually.
The Use mean value option is useful if the input voltage signal is noisy around a mean value. The Input Volts
value returned will be the mean value over the specified number of readings. When this option is selected, a
Settings button is activated and generates an Analog Channel Calibration prompt for the number of
readings.
The data is read the number of times indicated in the prompt and then the readings are averaged. The rate of
obtaining these readings is indeterminate because the rate depends on the actual hardware unit as well as the
communication type.
Increased Channel Count Support (AcqKnowledge 4.3 and above)
Previous versions of AcqKnowledge software supported a total maximum of 60 analog, digital and calculation
channels per graph. In AcqKnowledge 4.3, channel count capability has been greatly extended to a theoretical
maximum of 15,000 channels. While it is not generally feasible or useful to work with this many channels, it is
now possible to store and combine data derived from multiple hardware units, and perform complex specialized
analysis with data output to channels in the existing graph. (For example, advanced ICG analysis can potentially
add up to 20 additional channels to the existing total.)
When a large number of channels are present, the channel buttons appear in rows of 20 and will extend the
height of the channel toolbar to accommodate any increase in channel count.

Clicking into the right pane of the channel toolbar opens a contextual menu listing all channel numbers and
channel labels.

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Analog channels MP36R
The MP36R analog channel scaling setup works as shown above, but additionally allows the channel gain to be
configured directly with a variety of input ranges. Gain settings are accessible via a pop-up menu in the Channel
setup dialog. (MP36 > Set Up Channels) The Gain setting specifies the extent to which an incoming signal is
amplified. The Gain is automatically set when a data type is selected from the available Presets. The preset
Gain settings are only educated guesses and should be used as initial starting values. You may need to adjust the
gain settings depending on how the amplified signal appears once sample data is collected.

Offset
To correct the offset of an incoming analog signal, you can add or subtract a constant to the signal prior to
amplification. Offset can occur if a transducer or electrode has inherent offset. By default, Offset is set to zero,
and the allowable entry range will vary depending on the Gain and Scaling values.
To make inputting voltages easier, the analog channel scaling dialog for the MP36R displays the input voltages
in units that adapt to the gain setting. (x200 is the default)
The scaling units will adjust dependent upon the gain setting as follows:
- If the gain is set to < x1000, the Scaling input units will display as millivolts (mV).
- If the gain is set to > x1000, the Scaling input units will display as microvolts (V).


Channel gain set to < x1000 displays mV input units

Channel gain set to > x1000 displays V input units

Fixed Hardware Filters MP36R
The MP36R Unit allows up to three user-configurable, sequential, biquadratic (second order) Infinite Impulse
Response (IIR) filters. These filters are typically configured by choosing a Preset but can be changed manually
via the Input Channel Parameters dialog (MP36 > Set Up Channels > Setup button).
In the Digital Filters section, select Filter 1, 2, and/or 3 and then adjust the Type, Freq, and Q.
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Part C Analysis Functions 113

The default setting is no filters applied.
Adjustable Hardware Filters MP36R
These filters are implemented using resistors and capacitors in the front end circuitry of the MP36R unit. They
are set via the High Pass section of the Input Channel Parameters dialog (MP UNIT > Set Up Channels >
Setup).

High Pass Filter Appropriate use
0.05 Hz HP ECG
Respiration data
0.5 Hz HP ECG when there is a lot of motion artifact causing a shifting baseline
EEG
Pulse plethysmograph
Most other types of AC Coupled data
5 Hz HP EMG
Heart Sounds

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Additional controls in MP36R Input Channel Parameters
Button Explanation
New Channel Preset Allows a custom Preset to be saved under a unique name
Advanced Opens Advanced dialog. The Advanced dialog may be used to specify additional settings,
requirements, and dependencies for the preset. See below for complete explanation of all
Advanced options.
Scaling Use to configure the value of the incoming signal and how it will be plotted on the screen

MP36R Advanced Preset Settings
Click the Advanced button to open a dialog containing the following optional preset configuration options.

Acquisition Tab Explanation
Require minimum sampling rate When enabled, specifies that a minimum sampling rate must be selected
in order for acquisition to continue.

Transducer Tab Explanation
Verify connected
transducer
When enabled, the software will check for a specific transducer according to the settings in this
group box prior to the start of each appended segment
Title Editable text field used to identify transducer name.
SSID If checked, indicates which SmartSensor resistor ID should be validated for this channel prior to
each acquisition. The ID must be an integer between 1 and 23.
ISID Device Name If checked, indicates that the internal transducer description should be validated for this channel
prior to each acquisition.
Fallback on SSID if ISID
check fails
If the ISID device name check is unsuccessful for a connected transducer, fall back and check
the SmartSensor resistor ID.

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Part C Analysis Functions 115


Range + Grids Tab Explanation
Apply initial visual range The initial vertical axis range of plotted data will be set as indicated at acquisition start of the first
data segment.
Top Indicates the maximum vertical visual range in destination channel units.
Bottom Indicates the minimum vertical visual range in destination channel units.
Apply locked vertical
grid
Locked vertical grid settings are applied for the channel. For more details on grid setups, see
Grid Details on page 75.
First grid line Provides the fixed location of the origin of the vertical grid.
Grid spacing Sets the spacing interval between major vertical grid divisions.
Apply locked horizontal
grid
A channel-specific independent horizontal grid will be applied when the channel is added to a
graph.
First grid line Sets the origin location of the horizontal grids.
Grid spacing Sets spacing between major horizontal grid lines based on the time domain.
Apply grid appearance Enables options for setting grid color/appearance of major and minor grid lines.
Major line color Allows customization of major grid line color.
Minor line color Allows customization of minor grid line color.
Show minor grid Shows/hides minor gridlines
Vertical precision Indicates number of digits displayed on vertical axis.
Num minor divisions Sets the number of minor grid divisions for the channel.

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Calibration Tab Explanation
Use Calibration Additional calibration procedures will be applied to adjust the channel scaling based on
values read from a physical transducer.
Require calibration prior to
acquiring data
When checked, calibration will always be required for this channel prior to acquiring the first
segment of data.
Calibration Type Specifies calibration option to be performed on the channel. Two types are available:
- Single point records a single input voltage and adds it to the Input Volts value of
both Cal1 and Cal2
- Double point records two independent voltages in a sequence of two dialog
steps and records the first in the input volts for Cal1 and the second for the input
volts in Cal2

Prompt Displayed only for single point calibration.
Field for inputting dialog text to be displayed to the user for acquiring the single voltage
input to apply to the scaling input voltage values.
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Part C Analysis Functions 117
Digital channels
In contrast to analog channels, digital channels are designed to collect data from a signal source with only two
values (0 and 1). This type of data can be useful in recording whether a switch is open or closed, and
ascertaining if a device is on or off. Input values for digital channels have two values, +5 Volts and 0 Volts. The
MP150 interprets +5 Volts as a digital 1 and interprets 0 Volts as a digital 0. Since digital channels have a fixed
value, the scaling option is disabled for these channels. The main function of digital channels is to track on/off
devices such as push-button switches and/or to receive digital signals output by timing devices. Similarly, these
channels are also used to log signals from devices that output auditory/visual stimulus for examination of
stimulus response patterns.
0 volts
+5 volts
Positive edge Negative edge
(binary "1")
(binary "0")


Calculation channels
Compared to either analog or digital channels, Calculation channels do not collect external data, but transform
incoming data in some way. These channels do not alter the original data, but create new channels (with channel
numbers starting at CH40) that contain the modified data.
You can use Calculation channels to compute a host of new variables by using transformations (including BPM,
integration calculations, and math functions). The channels are Set Up in much the same way (using
Acquire/Plot/Values boxes) as analog or digital channels, with the exception of the pull-down menu next to the
Calc button and the Setup dialog.
To acquire a Calculation channel, click the Calc button and check the Acquire box for each Calculation channel
you want to compute (the Plot and Value boxes are optional). By default, all Calculation channels have the label
Calculation and entering more descriptive channel labels might prove useful, especially when multiple
Calculation channels are being acquired.
Each of these functions requires some additional parameters to be specified, and these options can be set by
clicking the Setup button in the Input Channels dialog. For any Calculation channel, you will (minimally) need
to specify the source channel to be transformed and the nature of the transformation.
Up to 16 Calculation channels can be acquired, and you may use the output of one Calculation channel as the
input for another channel, as long as the output channel has a higher channel number than the input channel. In
other words, its possible for Calculation channel 3 to include the result of Calculation channel 1, but not the
other way around. This allows for complex Calculations to be performed that involve two or more Calculation
channels such as filtering ECG data then computing BPM.
Although Calculation channels can be useful in many cases and indispensable in others, each Calculation
channel acquired will somewhat reduce the maximum possible sampling rate, and add to the amount of memory
required to store data both during and after an acquisition. Thus, you may want to consider performing some of
these functions after the fact if high sampling rates are needed for your particular application.
TIP: All of the operations (except Control) that can be performed online can
also be performed after an acquisition has been completed. These options
are available under the Transform and Analysis menus.

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Metachannel
Calculation metachannels provide a method for
expanding the 16 available calculation channels
to allow for more complex online analysis. The
metachannel calculation channel type combines
multiple steps into a single calculation channel
so that a chained computation can be
performed using a single calculation
metachannel.
- AcqKnowledge can display the results
of up to 16 metachannels, allowing for
a total of 256 intermediate subchannel
steps.

One metachannel can contain up to 16 subchannels, each of which can be individually configured. Subchannels
can perform any of the functions of top-level calculation channels.
Each metachannel has one user-defined output channel. The output subchannel is the only waveform data that
will be recorded in the graph for that metachannel. All other subchannels associated with that metachannel are
temporary; they do not display in the graph and require no extra space in the graph file to compute.
Metachannels alleviate the need to use top-level calculation channels for computing intermediate steps where
only the final computation is desired. Metachannels also can be used as the basis of presets, allowing multi-step
analyses to be applied with a single preset.
Computation takes place at the lowest waveform sampling rate of all of the referenced source channels, and all
subchannels are computed at this rate.
Metachannels labels display in the graph as C#.#
To have AcqKnowledge perform a Metachannel calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Metachannel.
5. Click the Setup button in the Input Channels dialog to generate the Metachannel dialog.

Primary Source
The primary source for a metachannel can be set to any analog, digital, calculation, or subchannel with a
lower index (index 0-15, with 15 being lowest).

Set Up Subchannel
Click this button to display the calculation setup dialog for the
selected subchannel and then set the calculation parameters
and the source channel.
Source channel: Each subchannel can be set to use the primary source channel as its data source or another
channel (analog, digital, or lower-index calculation channel). When the primary source channel for the
metachannel is changed, the source channel of each subchannel will implicitly be changed.
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Part C Analysis Functions 119
Limitations on Subchannels
Subchannels are allowed to take on any of the main calculation channel types. All calculation types are
available, with some restrictions.
- Output of reset events is not supported for Integrate and Rate subchannels.
- For Expression subchannels, the expression language will be enhanced to allow for "PSC" to be
typed into the expression to refer to the data of the primary source channel.
- Unlike regular calculation channels, the actual data for subchannels is not retained in memory.
Subchannels are only used as temporary data and the results discarded after the value of the
output subchannel has been computed.
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AcqKnowledge QUICK STARTS
Quick Start templates (.gtl graph template files) were installed to the Sample folder for PC users. You can use a
Quick Start file to establish the settings required for a particular application or as a good starting point for
customized applications. See Open As Graph Template on page 237 for details.
Q## Application(s) Feature
1 EEG
Sleep Studies
Real-time EEG Filtering
Real-time EEG Filtering
2 EEG Evoked Responses
3 EEG
Evoked Response
Event-related Potentials
Event-related Potentials
4 Evoked Response Nerve Conduction Studies
5 Evoked Response Auditory Evoked response & Jewett Sequence
6 Evoked Response Visual Evoked Response
7 Evoked Response Somatosensory Evoked Response
9 Evoked Response Extra-cellular Spike Recording
10 Psychophysiology Autonomic Nervous System Studies
12 Psychophysiology Sexual Arousal Studies
13 EBI
Cardiovasc. Hemodynamics
Exercise Physiology
Cardiac Output
Noninvasive Cardiac Output Measurement
Noninvasive Cardiac Output
15 EOG Nystagmus Investigation
16 EOG Saccadic Eye Movements
17 Plethsymography Indirect Blood Pressure Recordings
18A Plethsymography Arousal - Female
18B Plethsymography Arousal - Male
19 Sleep Studies Multiple-channel Sleep Recording
20 Sleep Studies
ECG
Cardiovasc. Hemodynamics
Online ECG Analysis
Online ECG Analysis
ECG Analysis
21 Sleep Studies SpO
2
Analysis
22 ECG Einthovens Triangle & 6-lead ECG
23 ECG 12-lead ECG Recordings
24 ECG Heart Sounds
25 Cardiovasc. Hemodynamics Online Analysis
26 Cardiovasc. Hemodynamics Blood Pressure
27 Cardiovasc. Hemodynamics Blood Flow
28 Cardiovasc. Hemodynamics LVP
31 NIBP Psychophysiology
32 In vitro Pharmacology Tissue Bath Monitoring
33 In vitro Pharmacology Pulsatile Tissue Studies
34 In vitro Pharmacology Langendorff & Working Heart Preparations
35 In vitro Pharmacology
Pulmonary Function
Isolated Lung Studies
Animal Studies
38 Pulmonary Function Lung Volume Measurement
39 Exercise Physiology Respiratory Exchange Ratio
40 EMG Integrated (RMS) EMG
41 EMG EMG and Force
42 Biomechanics Gait Analysis
43 Remote Monitoring Biomechanics Measurements
44 Biomechanics Range of Motion
45 Vibromyography Muscle Activity
46 Pressure Volume Loop Blood Pressure & Flow
47 Heart Rate Alarm Monitor heart rate with audible alarm
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Part C Analysis Functions 121
Chapter 6 Calculation
Channel Presets
Calculation Presets establish settings to target
application-specific analysis. Presets exist for a
broad range of analysis functions, including Fourier
Linear Combiners and Adaptive Filtering. Start
with existing presets for a specific species or
protocolfor example, human vs. small animal, or
stationary vs. exercising measurements.
The Channel Setup dialog contains a Preset pop-
up menu by each channel that lists the current
Preset or, if no Preset has been selected for that
channel, the Calculation type (Integrate,
Difference, etc.). When you select a Preset for a
particular channel, the channel is configured with
the settings associated with that Preset.
The Setup dialog has a Presets pop-up menu that
contains all of the Presets for the Calculation type
being configured. To enable the Preset pop-up
menu, set at least one analog channel to Acquire
(calculation channels require a source channel). For
example, if a Difference Calculation channel is
being configured, all Presets for the Difference
Calculation will be listed. Just click the Presets
head and scroll to select the desired preset.
When you select a Preset, the Setup dialog is
updated with the corresponding information.
The Setup dialog reads none if the
channel configuration doesnt match any
Preset. The menu will flip to none when
the settings for a channel are changed such
that they no longer match a Preset.
You can create a new Preset from existing
Calculation channels. Click Setup to
display the Calculation Setup dialog and
click the New Preset button. The settings
will be applied to the current channel, and
you will be prompted to enter a name for
the new Preset. You cannot duplicate a
Preset name, which also means that you
cannot use the default name of a
Calculation channel type (Integrate,
Difference, etc.). The new Preset will be
included in the pop-up menus and saved
with the file.
To reorder channel Presets (by type, use,
etc.), choose MP > Organize Channel Presets and then use the up/down buttons as appropriate
(see page 231).
Presets are not applicable to and therefore not selectable on Analog or Digital channels.
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Integrate Calculation

The online Integrate Calculation offers three basic options:
Reset via channel. Perform a real-time integration of input data over a variable number of sample points.
This option is extremely useful for converting flow signals into volumetric equivalents. The integral of flow
is volume. For example, when recording airflow with a pneumotach, volume can be precisely calculated as
the flow varies in a cyclic fashion:
a) Real-time conversion of flow signals into volume signals (i.e., Blood flow Blood volume; Air
flow Air volume).
b) Any processing involving a need for a cyclic, continuous integral calculated in real time. For
example: Acceleration Velocity; Velocity Distance; Frequency Number of cycles; Power
Energy.
Average over samples. Perform a moving average (mean) and associated processing (Rectify; Root mean
square) over the specified number of sample points. This option is useful to process EMG signals to:
a) Smooth noisy data
b) Display the real-time integration (rectified, then sample averaged) of the raw EMG data
c) Display the real-time root mean square calculation of the raw EMG data.
d) Return real-time windowed standard deviation.
Timed reset. This option is available in AcqKnowledge 4.1 and above in the Integrate calculation channel
and transformation. This mode computes a straight sum of the source data points and resets this sum after a
fixed amount of time has elapsed. This periodic integral is used in several types of analysis, such as EMG
analysis where it can generate an EMG signal or estimate the power in fixed time intervals. The time
interval at which the integral resets to zero may be specified in seconds or in samples. The timed integrate
reset functionality may also be used in calculation channel presets and by the Mac OS X Integrate
automator action.
To have AcqKnowledge perform an Integrate calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Integrate.
5. Click the Setup button in the Input Channels dialog to generate the Integrate dialog.
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Part C Analysis Functions 123
Destination
Determined by the calculation channel selected when the Scaling button was pressed.
Source
The source channel is selected from a popup menu that includes any channels being acquired and any
enabled Calculation channels.

Reset via channel (Integrate option)
This feature is used to integrate data over a data-dependent
interval. Either the source channel or a different channel can
control the integration process.
Control channel
Allows user to select any active channel as the integration
control channel.
Reset Thresholds
The threshold is to be set at points surrounding the flow
level. Typical values are:
LOW: a negative value close to 0.00
HIGH: a positive value close to 0.00
For airflow to volume conversion, the flow signal will vary
positively and negatively around zero flow.
Reset trigger
The Reset trigger polarity determines on which slope
(Positive | or Negative +) the integration process will begin
and end.
Mean Subtraction
This option will subtract the mean from the data evaluated during the integration period. If this option is
selected, the integration will only proceed after all the data in the integration period has been collected. When
collected, the mean value of all the data is subtracted from each data point in the integration period. In this
fashion, the integral of the corrected data points will result in the integral returning to exactly zero at the end of
the integration interval. Although this option will result in well-behaved integrations, the integrated data will
be delayed by a fixed amount of time, as specified by the max cycle period.
Online Enabling mean subtraction delays the signal by the mean cycle length. It waits for that period of
time to pass so it can determine a mean value for the initial cycle, and it then tries to re-compute
this mean for each cycle. If the resets are too short or too long, the window expires and the
processing halts again until a new mean can be recomputed. Online processing may reset from
threshold crossing in the control channel or window expiration when it loses mean tracking.
Offline Since all the data is available, the mean is computed from the data in the channel and the signal is
not delayed. Also, since it isnt doing windowed means, there are no window expiration events
that are inserted. Offline processing may reset from threshold crossing in the control channel.
Max cycle period
The Max cycle period should be longer than the maximum time expected from trigger event to trigger event in
the Control Channel. Typically, the default scale settings for cyclic integrated data will be fine. However, the
units may need to be changed (i.e., liters/sec to liters) via the Scaling option.
Output reset eventsnot available for metachannels
Add Events (markers) to show where Reset occurred and distinguish why the channel reached zero.
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Threshold crossing on the
control channel
For example: Calculation
channel resetting on positive
crossings of 0V on CH 1.


Window expiry when mean
removal is enabled
For example: No threshold
crossing within mean cycle
width as specified in calc
channel setup. Settings of
calc channel: threshold
crossings positive, 3V, Mean
cycle subtraction, 1 second
period width. First reset is
due to threshold crossing;
second reset is due to
window expiry.

Zero value due to true zero
being achieved due to
mathematical results
For example: Mathematical
Source is sine wave, integral
is cosine. Input (10V) never
crosses threshold levels.
Signal reaches zero
mathematically; no reset
events appear on output.


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Part C Analysis Functions 125
Average over samples (Integrate operation)
Online sample averaging can be useful when there
is a high degree of noise present in the data. At
least some of this noise can be averaged out by
pooling some number of adjacent data points
together, taking the average of these points, and
replacing the original values with the new averaged
values. This process creates a window of moving
averages that moves across the waveform
smoothing the data.

Integration used to smooth noisy data
Since an average represents the sum of a series of data points divided by the number of data points present, you
can use the Average over samples calculation to provide the information needed to create a moving average.
Samples
To specify the number of data points to average across, enter a value in the Samples box. The number you select
will depend in large part on the sampling rate you select and the type of noise present. All things being equal,
for slower sampling rates you will probably want to mean average across a smaller number of samples. As you
increase the sampling rate, you will probably want to integrate across more and more samples. As the number of
samples specified in the samples box increases, the amount of high frequency information contained in the data
will decrease.
Parameters
Rectify The Average over samples calculation
can also be used for producing an envelope of
modulated data. For instance, EMG waveforms
frequently contain high frequency information,
which is often of little interest compared to the low
frequency information also contained in the data.
When the Rectify option is checked,
AcqKnowledge will take the absolute value of the
input data prior to summing and a plot of the
waveforms mean envelope over a specified
number of samples will be obtained.

Online Average over samples feature used as an
envelope detector
Typically, this option is only used for processing raw EMG and similar types of applications. The signal for
Rectify is normalized by a factor of (# samples averaged)/(Channel sampling rate).
Root mean squareprovides the exact root mean square (RMS) of the input data (typically EMG) over the
specified number of samples.
Remove baselineprovides the exact standard deviation of the input data (typically EMG) over the specified
number of samples. When the mean of the input data equals 0-0, the standard deviation and the RMS will be
equivalent.
Scaling buttonSince the integration values are going to be on a different scale than the original units, you
need to change the scale of the integration channel to reflect the new units. When you click the Scaling
button, a Change Scaling Parameters dialog will be generated.
The rescaling involves multiplying the Input units values by a factor determined by the sampling rate and
number of samples mean averaged across.
Map or Scale value = Input units x
averaged mean be to samples of Number
rate Sampling

As an example, if data was being acquired at 75 samples per second, and you wanted to integrate across an
interval of 10 samples, you would set the Integration Setup Scaling parameters so that +10 Volts corresponded
to a Map (Scale) value of 75 and a Map (Scale) value entry of 75 reflected an Input value of 10 Volts.
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It is important to note that this rescaling should be performed independent of any rescaling performed
on analog channels themselves. Even if an analog channel is being rescaled to some other units, the
input values in the integration scaling should be set to +10 Volts (next to Cal 1) and 10 Volts (next to
Cal 2).

Integrate Calculation and Scaling dialogs for 10 point averaging
When data is averaged in this way, a portion of the data at the beginning of the record (equivalent to the number
of samples being integrated) should be ignored, as they will reflect a number of zero values being averaged in
with the first few samples of data.

Timed Reset (Integrate operation)

Timed Reset operation computes a straight sum of the source data points and resets this sum after a fixed
amount of time has elapsed. This periodic integral is used in several types of analysis, such as EMG analysis
where it can generate an EMG signal or estimate the power in fixed time intervals.
The time interval at which the integral resets to zero may be specified in seconds or in samples.
Timed reset functionality may also be used in calculation channel presets and by the Mac OS X Integrate
automator action.
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Part C Analysis Functions 127
Smoothing Calculation
The Smoothing Calculation functions online in real time and is very useful if you are trying to remove noise of
varying types from a data set.
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to
contain the filtered data. You may also check the Plot and
Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Smoothing.
5. Click the Setup button in the Input Channels dialog to generate
the Smoothing dialog.
(Off-line Smoothing is available under Transform > Smoothing.)

Source Source is a pull-down menu of the available channels.
Smoothing factor enter the number of samples to use as a smoothing factor.
Smoothing method This calculation channel provides real-time Mean (default) or Median smoothing.
Mean value The default is mean value smoothing. Use Mean value smoothing when noise appears in a
Gaussian distribution around the mean of the signal.
Use Median value Click in the box to activate Median value smoothing if some data points appear completely
aberrant and seem to be wild flyers in the data set.
For a given sequence of wave data, x = {x
1
, x
2
,...,x
n
}, Median value smoothing will sort the
sequence and extract the median equivalent to the recommended NIST (National Institute
of Standards and Technology) formula:
- n is odd: median is the center element of the sorted list of n items.
- n is even: median is the mean of the center pair of elements of the sorted list of n items.
The smoothing calculation channel is the primary method of computing real-time median
values using the definition of median as given above. The smoothing output at a sample
position is the median of the window of source channel samples including the current
sample and the previous samples in the window.
The size of the window is 1 at the start of acquisition and increases incrementally until
the final window size is reached. The median extraction method shifts between even and
odd definitions as the window size is incremented.
Scaling Click the Scaling button for access to options that allow you to modify the units or linearly
scale the output.

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Difference Calculation
The Difference calculation returns the difference between two data samples over a specified number of intervals
and divides the Difference by the time interval spanned by the data values. The Difference Calculation is useful
for calculating an approximation of the derivative of a data set in real time.
To have AcqKnowledge perform a Difference calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Difference.
5. Click the Setup button in the Input Channels dialog to generate the Difference dialog.
The Difference Calculation dialog allows you to specify the source channel and the number of intervals between
samples over which the difference is to be taken, and also includes the option of rescaling the channel to reflect
different units.
Click the Setup button in the Input Channels dialog to generate the Difference dialog:

Source When the Source channel contains relatively high frequency data, the Difference Calculation
may result in a very noisy response, so its best to use Difference on relatively smooth data.
Sample rate This line provides the sample rate for the selected channel (may be different than the
acquisition sample rate).
Intervals Difference is calculated with respect to the number of intervals between points (rather than the
number of sample points). For instance, two sample intervals span three sample points:
POINT<interval > POINT<interval > POINT
A 1-interval difference transformation applied to a blood pressure (or similar) waveform will
result in the widely used dP/dT waveform.
- See page 290 for a complete description of the online Difference function.
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Part C Analysis Functions 129
Rate Calculation

The Rate Calculation is used to extract information about the interval between a series of peaks in a waveform.
This interval can be scaled in terms of BPM (the default), frequency (Hz), or time interval between peaks.
The BPM (or beats-per-minute) Rate function is used as a measure of peaks or events that occur in a
sixty-second period.
The frequency rate function is commonly used to describe the periodicity of data, or the amount of
time it takes for data to complete a full cycle (from one peak to the next peak).
The Interval Rate function returns the raw time interval between each adjacent pair of peaks, which is
essentially the inter-beat interval (IBI), frequently used in cardiology research.
These three functions essentially provide the same information in different formats, since a frequency of 2Hz is
equal to an inter-peak interval of 0.5 seconds, both of which are equivalent to a BPM of 120. Other options
allow you to record the maximum or minimum value of all peaks (the peak max/min option), or to count the
aggregate number of peaks (the count peaks option).
In order to calculate Rate information, you have the option of specifying the threshold manually or having
AcqKnowledge automatically compute the default threshold value. This section describes the basic parameter
settings for typical online Rate Calculations.
NOTE: Parallel functions can be performed after data has been acquired. A
detailed description of the Rate Calculation options can be found in the Find
Rate section on page 324.

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To perform a Rate Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Rate.
5. Click the Setup button in the Input Channels dialog to generate the Rate dialog.
Sourceselected from the Source popup menu at the top of the dialog.
LabelUse to create a label for the Rate channel
PresetUse to select from 17 pre-defined calculation channel presets. New presets affecting source channel,
label and output settings can be created and saved by clicking New Channel Preset.
Signal Parameters Tab
Signal TypeContains parameters for specific human and animal waveform morphologies. Choose from six
pre-defined heart rate and respiration signal types, or click New to create and save custom setups. Unlike
channel presets, all pre-defined and custom signal types appear in both calculation channel Rate (online) and
analysis Rate (offline) dialogs. Signal type modifications affect settings in the Signal Parameters tab only. For
more details on Rate signal types, see page 327.
Peak DetectChoose whether to look for positive or negative peaks in the signal.
Remove baselineprovides the exact standard deviation of the input data (typically EMG) over the specified
number of samples. When the mean of the input data equals 0-0, the standard deviation and the RMS will be
equivalent.
Baseline window widthWidth of the window for the difference operation applied prior to peak detection.
(E.g. the value of the source x ms previously is subtracted from the current value to generate the signal that is
analyzed with the peak detection.)
Auto Threshold detectThe most convenient way to calculate a Rate channel online is to have
AcqKnowledge automatically compute the threshold value (the cutoff value used to discern peaks from the
baseline). This is done by checking the Auto Threshold detect box.
Noise rejectionAcqKnowledge constructs an interval around the threshold level when Noise rejection is
checked. The size of the interval is equal to the value in the noise rejection text box, which by default is equal to
5% of the peak-to-peak range. Check this option to help prevent noise spikes from being counted as peaks.
Cycle Interval WindowWhen automatic Rate Calculations are set, specify a minimum rate and a
maximum rate. These parameters define the range of expected values for the Rate Calculation. By default, these
are set to 40 BPM on the low end and 180 BPM on the high end.
The Rate Calculation will use these values to find and track the signal of interest, assuming the input BPM
range is reasonably well bracketed by these values. Depending on the shape of the input cycle waveform, the
Rate window settings may be closer or further from the expected rates.
For ECG-type data (where the waveform peak is narrow with respect to the waveform period), the
Rate window values will closely bracket the expected values.
For more sinusoidal data, with the waveform energy distributed over the waveform period (as with
blood pressure or respiration), the Rate window will closely bracket the expected rate on the high-end,
but can be up to twice the actual measured rate at the low-end.
One of the most frequent applications of the Rate Calculation is to compute BPM online for
ECG, pulse, or respiration data. For more information on optimizing ECG amplifiers for online
calculation of heart rate, see the ECG100C section of the MP Hardware Guide.
Windowing UnitsUse to select the unit type to be used in the rate detection. The options are Hz, BPM and
seconds.
Output Tab
Function The popup menu includes options to scale the rate in terms of Hz, BPM, Interval, Peak Time,
Count Peaks, Peak Minimum/Maximum, Peak-to-Peak, Mean Value, or Area.
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Part C Analysis Functions 131
For more information on each of these functions, see the Calculation Channels section beginning on
page 117.
Calculate systolic using the peak maximum Function, diastolic using the peak minimum Function, and
mean blood pressure using the mean value Function.
NOTE: All of these Function options are available in the post-acquisition mode through
the Analysis > Find Rate function.
Use Averaging modeUse to average to output of the selected function. Averages can be based upon a fixed
time window or a fixed number of cycles. The Recompute on every cycle option will start the averaging
output after N numbers of cycles are detected and then remain fixed until the next N cycles are detected.
Output reset events (not available for metachannels)When auto threshold detection is being used, the
minimum and maximum rates of the signal are specified in the Windowing controls. If the input signal falls out
of this range, the value of the rate function and automatic threshold level will be reset. By enabling Output
reset events a reset event will be placed on the output at the location of these window expirations. Rate
detector is set to Peak function, default window of 40 BPM to 180 BPM, auto threshold detect for positive
peaks. The reset event occurs after the window expiration, approximately a full 40 BPM interval after the
peak transition from 0 to 5 volts in the source signal.

Show ThresholdPlots the threshold used by the Rate calculation function. This feature is useful to help the
rate detector performance on any given data.
Show ModifiedPlots the modified data as processed by the Rate Detector. Typically, the modified data is a
differential version of the original input data. The data will be modified if the remove baseline feature is
checked in the Rate Detector Setup dialog.
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Math Calculation
The Math Calculation performs standard arithmetic calculations using two waveforms or one waveform and a
constant. It is also possible to use other Calculation channels (such as a Rate Calculation channel) as an input
channel for a Math Calculation channel, as long as the Calculation channel used as a source channel has a lower
channel number than the Math Calculation channel.
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Math.
5. Click the Setup button in the Input Channels dialog to generate the Math dialog.
Use the pull-down Source menus to select the source channels (Source 1 and Source 2).
The Sample rate line provides the sample rate for the channel selected as Source; the channel sample rate may
be different than the acquisition sample rate.
Use the pull-down Operand menu to select a function. In the example below, analog channel 1 (Source: A1) is
added to analog channel 2 (Source: A2). To use this summed waveform as an input for another Math
Calculation channel. One useful application would be to divide this waveform (C0) by K, where K=2, thus
producing an arithmetic average of source channels A1 and A2.

The Constant entry is activated when K is selected as a Source.
As an alternative to creating an additional Calculation channel for dividing the summed waveform, you can use
the scaling function to perform the same task. To do this, click Scaling button and then set the Map (Scale)
value for the summed waveform equal to +5 and 5 (to correspond to Input Volts values of +10 and 10
respectively). This will effectively plot the sum of channels A1 and A2 as the arithmetic mean of the two
waveforms.
For additional libraries of online Calculation options, consult the sections on Function Calculation
channels and the online Expression, page 136). These types of Calculation channels can be used to
perform more complex operations on waveforms. Although Calculation channels can be chained
together (so that the output from one serves as the input for another) to form more complex
calculations, a separate channel must be used for each function. Since only sixteen Calculation channels
are available, not all calculations can be performed. Additionally, chaining more than three or four
channels together can require considerable system resources.
For complex calculations (such as squaring a waveform then adding it to the average of two other
waveforms) the Expression is a more efficient solution. All of the features available online in the Math
Calculation channels can also be computed after an acquisition using the Waveform Math option (see
page 293), which will eliminate the problem of system overload.
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Part C Analysis Functions 133
Function Calculation


The Function calculation can be used to perform a variety of
mathematical functions using two waveforms or a waveform and a
constant. Function Calculation channels compute new waveforms
in a manner similar to the math Calculation functions, but provide
access to higher order functions. Like math Calculation channels,
function Calculations can be chained together to produce complex
functions (such as taking the absolute value of a waveform on one
channel and Calculating the square root of the transformed
waveform on another channel). These same functions are also
available under the transform menu in AcqKnowledge for post-hoc
operations. Many of these functions can also found in the online
Expression, see page 136 for details).
To have AcqKnowledge perform a Function Calculation in real
time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you
want to contain the filtered data. You may also check the
Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Filter.
5. Click the Setup button in the Input Channels dialog to
generate the Function dialog.
Other Functions are available in the online Expression (see page
136). Function Calculations can be chained together to produce
more complex Calculations, although it is more efficient to
program complex functions using the Expression calculation.
The Sample rate line provides the sample rate for the selected
channel (may be different than the acquisition sample rate).
Function
Abs Returns the absolute value of each data point
Atan Computes the arc tangent of each data point
Exp Takes the e
x
power of each data point
Limit Limits or clips data values that fall outside specified boundaries
Ln Computes the base e logarithm for each data point
Log Returns the base 10 logarithm of each value
Noise Creates a channel of random noise with a range of 1 Volt
Sin Calculates the sine (in radians) of each data point
Sqrt Takes the square root of each data point.
Threshold Converts above an upper threshold to +1 while converting data below a lower threshold to 0.
Thresholding Algorithm Assume a domain variable

t e t
start
, t
start
+1, t
start
+ 2, { }
with t
start
being an integer, a real-valued signal y(t) defined for all t, and two real valued levels y
low

and y
high
satisfying the relation y
low
s y
high
.
Define the Threshold function thresh(t) function such that:
thresh(t
start
) =
start low
0 y(t
start
) < y
low
1 y(t ) > y


thresh(t) =
0 y(t) < y
low
1 y(t) > y
high
thresh(t 1) y
low
s y(t) s y
high






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Filter Calculation
The Filter Calculation channel allows you to perform real time digital filtering on analog, digital, or calculation
channels. To have AcqKnowledge apply a digital Filter Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Filter.
5. Click the Setup button in the Input Channels dialog to generate the Filter dialog.

Filter Setup & Output Options
In the dialog above, the signal on analog channel one (A1) is run through a low-pass filter that attenuates data
above 50 Hz. The Q for this filter is 0.707, which is the default.
One possible application of the online filtering option is in conjunction with the Show Input
Values option (see page 218). Raw EEG data, for instance, can be filtered into distinct
bandwidths (alpha, theta, and so forth) using one source channel and multiple filter Calculation
channels. The filtered data can then be displayed in a bar chart format during the acquisition
using the Show Input Values option.
Source Set the source channel.
Sample rate provides the sample rate for the selected channel (may be different than the acquisition sample
rate).
Type (Output) Lists the filter options: low pass, high pass, band pass, band pass (low + high), band stop, and
comb band stop. See About Filters in this section for more details on filter types.
Frequency Fixed valueType a value in the entry box.
Sampling rateSets the frequency to a fraction of the sampling rate and automatically updates
when the sample rate is modified.
Line frequencyUses the line frequency at which the data was recorded.
Q coefficient The online filters are implemented as IIR (Infinite Impulse Response) filters, which have a
variable Q coefficient. The Q value entered in the filter setup box determines the frequency
response patterns of the filter. This value ranges from zero to infinity, and the optimal
(critically damped) value is 0.707 for the Low pass and High pass filters, and 5.000 for the
Band pass and Band stop filters. If you wish, you may change the Q. A more detailed
explanation of this parameter and digital filters in general, can be found in Appendix B.
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Part C Analysis Functions 135
About Filters
While the technical aspects of digital filtering can be quite complex, the principle behind these types of filters is
relatively simple. Each of these filters allows you to set a cutoff point (for the low and high pass filters) or a
range of frequencies (for the band pass and band stop filters).
A Low Pass filter allows you to specify a frequency cutoff that will pass or retain all frequencies
below this point, while attenuating data with frequencies above the cutoff point.
High Pass filters perform the opposite function, by retaining only data with frequencies above the
cutoff, and removing data that has a frequency below the specified cutoff.
Each type of Band Pass filter is optimized for a slightly different type of task.
The Band Pass (low + high) filter is designed to allow a variable range of data to pass through the filter.
For this filter, you need to specify a low frequency cutoff as well as a high frequency cutoff. This
defines a range or band of data that will pass through the filter. Frequencies outside this range are
attenuated. The Band pass (low + high) is actually a combination of a low pass and a high pass filter,
which emulate the behavior of a band pass filter. This type of filter is best suited for applications where
a fairly broad range of data is to be passed through the filter. For example, this filter can be applied to
EEG data in order to retain only a particular band of data, such as alpha wave activity.
The alternative Band Pass filter requires only a single frequency setting, which specifies the center
frequency of the band to be passed through the filter. When this type of filter is selected, the width of
the band is determined by the Q setting of the filter (discussed in detail below). Larger values for q
result in narrower bandwidths, whereas smaller Q values are associated with a wider band of data that
will be passed through the filter. This filter has a bandwidth equal to Fo/Q, so the bandwidth of this
filter centered on 50 Hz (with the default Q=5) would be 10 Hz. This type of filter, although
functionally equivalent to the band pass (low + high) filter, is most effective when passing a single
frequency or narrow band of data, and to attenuate data around this center frequency.
The Band Stop performs the opposite function of a band pass. A Band stop filter defines a range (or
band) of data and attenuates data within that band. In this case, the Band stop filter is implemented in
much the same way as the standard Band pass, whereby a center frequency is defined and the Q value
determines the width of the band of frequencies that will be attenuated.
The Comb Band Stop removes interfering harmonics; resonance, aliasing, and other effects may
generate interference at multiples of a base frequency. It combines all the required filters instead of
requiring a separate filter for each interfering overharmonic. For setup details, see page 271.
Off-line filtering
Apart from these online filter options, similar filters can be applied after an acquisition is terminated. Many of
the biopotential amplifiers available from BIOPAC have selectable filters, which allow you to filter certain
frequencies (including 50 Hz or 60 Hz electrical noise) and possibly reduce the need for online filters.
Digital filtering can also be performed after an acquisition using the same types of filters. You can choose from
the different filter types by selecting Digital filters from the Transform menu. The filters available after the
acquisition use a different algorithm but operate in essentially the same way.
For more information on digital filters and filters that can be applied after an
acquisition, turn to the Digital Filtering section on page 265 or Appendix B.
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Expression

The online Expression calculation channel is available for performing computations more complex than possible
in the Math and Function calculations. The Expression calculation will symbolically evaluate complex
equations involving multiple channels and multiple operations. AcqKnowledge can perform conditional
evaluation, data extraction, logical operations, expressions requiring a range of samples or the results of the
previous expression, and evaluation of generic formulas that can be expressed in a closed, recursive form.
Unlike the Math and Function calculationswhich can only operate on one or two channels at a timethe
Expression calculation can combine data from multiple analog channels, and allows you to specify other
Calculation channels as input channels for Equation channels. Also, computations performed by the Expression
calculation eliminate the need for chaining multiple channels together to produce a single output channel.
While the Expression calculation is more powerful than other Calculation channels, each Expression calculation
requires more system resources than other Calculations. This essentially means that acquisitions that utilize
Equation calculations are limited to a lower maximum sampling rate than acquisitions without online
Expression functions. When an expression is evaluated, it is actually evaluated multiple times. The expression is
computed starting at the first sample acquired, and is then evaluated once for each successive acquired sample.
AcqKnowledge can accept the notations SC, MC, and CHn to reference the sample at the current evaluation
position or SC( x) , MC( x) , and CHn( x) for values at locations prior to the present evaluation location using
an offset expressed in sample intervals. For example, CH1(-1) will give the previous sample of Channel 1.
The same features that are available in online Calculation channels are also available under the Transform menu
for evaluation of complex equations after acquisition. Thus, simple Calculations such as summing two channels
or dividing one channel by another (and so forth) are best performed in either the Math calculation channels or
the Function calculation channels.
On the other hand, for complex Calculation channels, such as squaring one channel, multiplying it by the sum
of two other channels, and dividing the product by the absolute value of another waveform, a single Expression
calculation channel is more efficient than chaining five Math and Function calculation channels.
Save to Calculation Channel
To evaluate an expression and save the result to a Calculation channel in real time:
1. Choose MP> Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Expression.
5. Click the Setup button in the Input Channels dialog. This will produce a dialog, where you can enter the
expression to be evaluated.
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Part C Analysis Functions 137
The different components of each expression can be entered either by double-clicking buttons from the button
rows (sources, functions, and operators) in the setup expression dialog, or by typing commands directly into the
Equation box. The Expression calculation uses standard mathematical notation.
For each expression, you need to specify at least one source, the function(s) to be performed, and any operators
to be used. Sources are typically analog channels, although you may also select Time from the source button
row and AcqKnowledge will return the value of the horizontal axis (usually time) for each sample point. When
the horizontal axis is set to frequency (in the Display > Horizontal axis dialog), the time item in the source
button row will switch to frequency.
When using the online Expression calculation channel, it is important to keep in mind that while different
channels, functions, and operators can be referenced, the Calculation cannot reference future sample points.
That is, data from waveform one can be transformed or combined in some way with data from waveform two at
the same point in time, although data from one point in time (on any channel) cannot be combined with data
from another point in time (on any channel). See the section on post-acquisition expression commands
(beginning on page 292) for ways around this limitation.
Functions The arguments to each function are represented in the Functions table in italics and may
be replaced by any valid expression. Each argument is separated from its next argument
by a comma. Expressions can only contain commas within balanced parenthesis pairs. An
ellipsis (...) at the end of a function description indicates that any number of arguments
may be present provided they are in a comma separated list. When a function is added to
an Expression, the cursor is placed between the parentheses.
Conditionals Change output based upon a condition test. All of the conditionals treat the value zero as
false and any non-zero value as true. Expressions can only contain commas within
balanced parenthesis pairs.
Offset Notation Offset notations take integer offsets in terms of the number of samples using the
formation CH#(P) where CH# is the channel number and P is the number of points. For
example, an offset of -1 will return the data point immediately to the left of the selected
point and an offset of +1 will return the data point immediately to the right of the selected
point.
To refer to previously acquired data, offsets must be negative. For notational
convenience, offsets that result in an invalid negative sample position (e.g. no data is
defined prior to the first sample in the graph) evaluate to zero. Any attempt to access a
sample beyond the end of the data will result in an error. Any attempt to use a positive
offset for an online Expression calculation channel will result in an error.
CHn( x) Returns the value of channel with index n x samples away from the current
evaluation position.
SC( x) Returns the value of the selected channel x samples away from the current
evaluation position. Only allowed for Transformations and Measurements; not
allowed for Calculations.
MC( x) When x is zero or positive, returns the value of the measurement channel x
samples away from the current evaluation position. When x is negative, returns
the result of the expression evaluation that occurred x steps previous to the
current evaluation position. Only allowed for Measurement Expressions (see
below); not allowed for Calculations or Transformations.
Recursive notation Since transformations and calculation channels replace the source data of the channel
with the result of the expression evaluation in sequence, negative offsets are equivalent to
returning the final result of the expression that was evaluated a certain number of steps in
the past. The channel where the expression results are stored can be thought of as a
storage record of the previous evaluation steps. Negative sample offsets, therefore, can be
used to compute any formula that can be expressed in closed recursive form. For
example, the recursive definition of the Fibonacci sequence is:
F
n
= F
n-1
+ F
n-2

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To evaluate this as an expression transformation, use the expression:
SC(-1)+SC(-2)
Note that to actually get the Fibonacci sequence; the selected channel would need to have
a constant value of one prior to the transformation.
Expression Measurements are powerful tools for quick manual analysis and also for advanced
Measurement automated analysis when combined with the Cycle/Peak detector. Expression
measurements extend measurements to evaluate simple formulas or complex data
reduction. Each Expression measurement has an expression associated with it and the
measurement result is derived from computing the Expression(s) on the selected data.
Measurement expression dialog is
generated the first time a measurement is
set to Expression or when the
measurement preset button is clicked.
Preset menu allows access to pre-loaded
commonly used expressions and displays
user-defined custom presets, along with a
list of recently-used expressions.
OK invokes a syntax check. If there is an
error, the user will be prompted to
correct the error and the error will be
selected (highlighted) in the Expression
edit field.
Cancel discards any changes to the
Expression measurement and reverts
back to the previous Expression.
Clear erases the current contents of the
expression edit field.

Measurement Channel
Expression measurements can reference the measurement channel (MC), which refers
to either the selected channel or a specific channel as set in the measurement channel
selection box within the graph window.
Negative sample offsets to MC are interpreted as returning the result of the Expression
from a prior step. Transformations and calculation channels achieve this as they replace
the contents of their destination channels sequentially. Measurements, however, do not
actually replace the data of their source channels. Expression measurements are actually
executed on a temporary copy of the channel data in memory. This implies that negative
indicies to the measurement channel are interpreted exactly the same for measurements as
for transformations and calculation channels even though the transformed data of the
measurement is not visible. Negative sample offsets to MC that refer to the sample
position prior to the leftmost sample of the selected area will always return zero.

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Part C Analysis Functions 139
Evaluation Rules
When a new selection is made, the first step in evaluation searches through the
Expression measurement for any MMT() invocations. Any measurement whose value is
needed by MMT() is computed at this time prior to the Expression evaluation. This
behavior is similar to calculation channels and successfully allows measurements to the
right and bottom of the Expression measurement to be used in the expression.
The expression is subsequently evaluated from the leftmost sample in the selection to the
rightmost sample. It is evaluated at the waveform sampling rate of its source channel,
with one expression evaluation per sample contained within the selected area.
Interpolation is not used at the boundaries to maintain a consistent sample interval for the
expression. After each expression evaluation, the result is cached in memory for potential
negative MC result references.
The value of the final expression, the rightmost sample, becomes the result of the
measurement.
Circularity Detection
Expression measurements may reference other expression measurements or calculation
measurements by using the MMT() function in the expression. This raises the possibility
of circular dependencies being formed by the user if a measurement expression either
directly or indirectly needs its own value to compute a MMT() invocation. Circular
dependency checking will be in place at execution time and will result in an error.
To refer an Expression measurement to its own value, use the MC notation.
Error Reporting
The Expression measurement result will display the text Error if there are syntax errors
in the Expression measurement, errors computing measurements referenced by MMT(),
or a circularity.
Validation Tip To function correctly, AcqKnowledge requires real-valued data. You are encouraged to
ensure that your expression results are real-valued. To test if a floating point number x is
a real-valued number, use the expression:

NOT(OR(ISINF(x), ISNAN(x)))
Note for variable sample rate processing:
The Expression and Waveform Math functions will constrain operations between waves of different rates as
follows:
If an equation is operating on two or more waves of different sample rates, the result of the operation will always
be output at the lowest sampling rate from the waves (F low). If the destination channel for the result has an
assigned rate other than (F low), the operation will not be permitted. If the destination channel is set to a new
channel, the operation will always be permitted.
In AcqKnowledge 4 and higher, all sources for Expressions and Waveform Math operations must be sampled at
the same waveform sampling rate.
VSR data paddingIf the channels are of unequal length (as a result of variable sampling rate or waveform
editing), they will be padded for Append acquisition. Digital and Analog channels are stored as short integers by
default; a waveform paste into a digital or analog channel, however, will result in its underlying data being
converted to floating point. This will generate the Abort/Replace warning for pastes to Digital or Analog
channels since the data format has changed since the last acquisition.
Additionally, if an Analog or Digital channel is used as the source waveform for a Copy, it will also be converted
to floating point and will result in the Abort/Replace warning being generated.
Since Calculation channels are already floating point, pasting into them or copying from them will not change
their data format. The channels will be padded with their last value and the append will commence.
Waveform Cut operations do not change the underlying data format for Analog, Calculation, or Digital channels.
If only Waveform Cut is used, no data format conversion will occur and channels will be padded with their last
value and subsequent appends are allowed.
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Source Description
ACQLENGTH

Calculation only Acquisition length from
Set Up Acquisition; keeps Appended
segments the same whereas Sample
would increase with each segment.
CH Value of the designated channel (CHn) at
the current evaluation step.
Primary Source
Channel
metachannels only
Appears as PSC in the dialog. Refers to
the data of the primary source channel of
a metachannel.
Time
Time (in sec) of current evaluation step
Sample Sample index of evaluation step; the first
sample in the graph will always be
reported as a value of zero.
MC Measurements only Value of the channel in
the measurement menueither the
explicit channel or SCat the current
evaluation step.
Pi Value of pi (3.141592654) to double-
precision accuracy.
SC

Transformation and measurement only Value
of the selected channel at the current
evaluation step; can still back-reference
samples points.
True Evaluates to the value 1 (non-zero values
are interpreted as True)
False Evaluates to the value 0
Segment Timer Used as a source for the onscreen
Stopwatch gauge view.
Random Generates random white noise.
Gaussian
Random*
Generates Gaussian white noise for
startle responses. Returns a random
value from a Gaussian distribution.
*Standard Gaussian model; useful for peak fitting.
param(0)*EXP(-((TIME-param(1))/param(2))^2
Operator Operation
+ Addition
- Subtraction
* Multiplication
/ Division
^ Power
( Open parentheses
) Close parentheses
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Part C Analysis Functions 141
FUNCTION RESULT
ABS Returns the absolute value of each data point.
ACOS Computes the arc cosine of each data point in radians.
AND(x, y, ) Computes a logical and operation for its arguments. Accepts up to eight (8)
arguments and evaluates to
1 if all of its arguments are non-zero values.
0 if one of its arguments is zero.
ASIN Calculates the arc sine of each value in radians.
ATAN Computes the arc tangent of each sample point.
CEIL(x) Computes the ceiling function (the closest integer larger than the value x).
COND(T, A, B, C) Three-way conditional takes four arguments:
COND(test_expr, neg_test_value, zero_test_value, pos_test_value)
Evaluates test_expr and if
< 0, returns neg_test_value
= 0, returns zero_test_value
> 0, returns pos_test_value
COS Returns the cosine of each data point.
COSH Computes the hyperbolic cosine of each selected value
EQUAL(x, y, ) Performs a Logical equal (numerical comparison) of its arguments. Accepts up to
eight (8) arguments and evaluates to
1 if all of its arguments are equal.
0 if one of its arguments is not equal to the others.
EXP
Takes the e
x
power of each data point..
FLOOR(x)

Computes the floor function (the closest integer less than the value x).
IF(T, A, B)

Two-way conditional takes three arguments:
IF(test_expr, true_value_expr, false_value_expr)
The conditional evaluates test_expr and if
non-zero, returns true_value_expr
0, returns false_value_expr
ISINF(x) Filters out infinities and unrepresentable numbers from data; important because
such values can cause erratic behavior in autoscaling and other operations. Use to
test whether any expressions have resulted in floating point overflow and have
generated numbers too large to be represented in the computer. Evaluates to
1 if x is inf, the floating point representation of infinity.
0 if x is NaN or a real-valued floating point number.
ISNAN(x)

Is not a number can be used to test whether any expressions have resulted in
floating point errors such as division by zero. Use to ensure that the output of
transformations and equations does not produce numbers that AcqKnowledge
cannot display. Evaluates to
1 if x is NaN, the invalid floating point number.
0 if x is inf or a real-valued floating point number.
LESS(x, y)

Performs a numerical comparison of its arguments and evaluates to
1 if x is less than y.
0 if x is greater than or equal to y.

LOG Computes the natural logarithm of each value
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LOG10 Returns the base 10 logarithm of each value

FUNCTION RESULT
MMT(row,col) Transformation and measurement only Evaluates to the result of a measurement
being displayed in the graph, as specified by row and column. Use to scale by a
result without having to manually enter the result. Row and Column for a
measurement start as 0,0 for the top left measurement box; the fourth argument on
the first row is accessed by MMT(0,3). For this function, the required measurement
box must be displayed in the graph. Since the values of measurements may change
during the course of an acquisition, calculation channel expressions cannot use this
function.
If a Model Expression (page 297) uses MMT() syntax to reference a measurement
and that referenced measurement is linearly interpolated, the results of the NLM
measurement will also be displayed as being linearly interpolated.
MOD(x,y) Computes the floating point modulus; returns integer portion of modulus.
Example: MOD(5,2) evaluates to 1
NOT(x) Computes a logical negation of its argument. Evaluates to
1 if x is zero.
0 if x is non-zero.
OR(x, y, )

Evaluates multiple variables; true if any are true. Computes a logical or operation
for its arguments. Accepts up to eight (8) arguments and evaluates to
1 if any one of its arguments is non-zero.
0 if all of its arguments are zero.
ROUND(x)
Returns an integer closest in value to the argument. For example:
round (2.4) = 2 round(2.5) = 3 round(-1.5) = -1 round(-1.6) = -2
SIN Calculates the sine (in radians) of each data point.
SINH Computes the hyperbolic sine for each sample point.
SGN Performs the sgn sign extraction function. Evaluates 1 if x > 0, -1 if x = 0, and 0 if x
= 0.
SQR Squares each data point.
SQRT Takes the square root of each data point.
TAN Computes the tangent of each sample point.
TANH Calculates the hyperbolic tangent of each sample point.
TRUNC(x)
Removes the fractional part of the number and returns an integer. For example:
TRUNC(2.4)= 2 TRUNC(2.5)= 2 TRUNC(-1.5)= -1 TRUNC(-1.6)= -1
Note When used with scientific notation, TRUNC(x) applies only to the fractional
portion after the exponential factor is taken into account: TRUNC(2.93E+4) =
TRUNC(29300) = 29300. Since 2.93e+4 (29,300) has no fractional portion,
the number is returned unchanged. Similarly, TRUNC(2.931245E+4) =
TRUNC(29312.45) = 29312.
XOR(x, y, ) Logical exclusive OR; true if an odd number is true. Computes a logical exclusive
or for its arguments (e.g. one or the other, but not both). Accepts up to eight (8)
arguments and evaluates to
1 if an odd number of its arguments are non-zero.
0 if an even number of its arguments are non-zero or
if none of its arguments are non-zero.

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Part C Analysis Functions 143
Delay Calculation


Delay setup dialog and resulting graph showing a 20 sample delay
This option allows you to use a Calculation channel to plot another channel lagged (delayed) by an arbitrary
interval. To have AcqKnowledge apply a Delay Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Delay.
5. Click the Setup button in the Input Channels dialog to generate the Delay dialog.

The delay interval can be specified either in terms of samples or seconds. These types of plots are useful for
producing non-linear (chaos) plots in AcqKnowledges X/Y display mode (see page 37 for a description).
When a delay channel is recorded, there is a segment at the beginning of the Calculation channel (equal to the
value of the delay) that will read as 0 Volts. This is normal and occurs because the delay channel is waiting to
catch up with the original signal. AcqKnowledge fills this buffer with zeros until the delay channel begins to
plot actual data. In the example below, the delay channel contains a 0.25-second interval of zeros at the
beginning of data file.
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Control Calculation

The Control function is used to output a digital pulse when the value for a specified input channel exceeds a
certain level, falls inside a given range, or falls outside a given range. This feature is unique in that the output is
on a digital channel (which ranges from I/O 0 through I/O 15) rather than a Calculation channel. Also, unlike
other Calculation channels, this Control Calculation can only be performed in real time (i.e., while data is being
acquired) and cannot be performed in post acquisition mode.
In addition to outputting a signal on a digital channel, the Control Calculation will also plot an analog version of
the digital signal on the Calculation channel you specify. For instance, in the example below, Calculation
channel C0 is used to perform a control function using analog channel 1 (A1) as an input and digital channel 0
(D0) as an output. In addition to outputting a pulse on D0, the setup below will also produce a plot on channel
40 (the first Calculation channel) that emulates the signal being output on digital channel 0. Since Calculations
are analog channels, the Calculation channel does not contain a true digital signal, but is a reasonably good
approximation. To retain the physical output generated by a Control channel, the output digital channel should
be looped back to another digital input channel of the MP unit and acquired as well as being connected to any
external devices. The calculation channel values are not guaranteed to precisely match the actual digital output.

To have AcqKnowledge apply a Control Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Control.
5. Click the Setup button in the Input Channels dialog to generate the Control dialog.

There are four parameters that need to be specified for each Control channel:
a) Source channel c) Type of threshold function
b) Output channel d) Threshold level values
Source refers to the input channel to be used for the Control function. As with other Calculation channels, the
Control function can use either an analog channel or another (lower) Calculation channel as an input. In the
previous example, analog channel 1 (A1) is used as the input channel. It is not possible to use a digital channel
as an input channel for a Control Calculation.
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Part C Analysis Functions 145

The channel selected in the Output Channel section determines which digital channel the pulse will be sent to.
The digital channels range from 0 to 15 (D0 through D15) and external devices can be connected as described
in the section on UIM100C connections in the MP System Hardware Guide. In the sample dialog shown, the
digital pulse is sent over I/O line D0.
Digital channels have two levels, 0 Volts and +5 Volts. When the signal transits from 0 Volts to 5 Volts, an
edge is created and since the signal is going from low to high, this is referred to as a positive edge. Similarly,
as the signal transits back from 5 Volts to 0, a negative edge is created. These transitions or edges can be used to
trigger external devices when an analog signal level meets certain threshold criteria.
The Threshold Function option sets the criteria for the Control channel. You can specify threshold conditions
such that the digital I/O line goes to +5 Volts when the conditions are met, or you can program the digital line to
go to 0 Volts when the threshold conditions are met. Threshold conditions can be set so that either (a) the digital
line is switched when the value of an analog channel exceeds a specified value or (b) the digital line is switched
when an analog channel falls within a given range. AcqKnowledge also allows you to create a single level
threshold or a wide threshold.
Tip To use test conditions more complicated than simple thresholding, combine the conditional tests of
Expression calculations with the Control channel to change digital output based on the Expression
result.
For example, suppose you want to set a Control channel to switch digital line 5 from low to high whenever the
signal for Calculation channel one (C0) exceeds 85 BPM. Set the source channel to C0 and the output to D5.
Select the upper left graph in the control dialog and set L2 and L1 to 85, as shown:

Control dialog and graph showing result of BPM control example
As you can tell from the preceding graph, there are a number of instances where C0 (heart rate) exceeds 85,
usually for a short period of time. When it does drop below 85, it appears to return to a value greater than 85
within a second or two. In instances such as this, it might be useful to widen the threshold so that the digital
line is triggered whenever the input value is greater than 85, but the signal must drop significantly below the
threshold value before the threshold is reset.
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As another example, the upper threshold value (L2) is set to 85 and the lower threshold (L1) is set to 83, which
means that the threshold will not reset until the signal from the source channel drops below 83. In the following
example, the digital line is switched from low to high (from zero to +5 Volts) when the heart rate channel
exceeds 85, and stays at +5 Volts for several seconds even though the source channel drops below 85 (but above
83). The digital line does not switch back to zero until the heart rate channel drops below 83 (toward the end of
the record). Once this occurs, the threshold is reset and the digital line will switch again the next time the source
channel exceeds 85 BPM.

Control dialog and graph showing control channel with wide threshold
It is also possible to have the digital line switch when the source channel drops below a certain value. In the
example below, a simple threshold is used to switch the digital line high each time the source channel drops
below 50 BPM. Since L2 and L1 are set to the same value, this is not a wide threshold (as above) and the
threshold resets each time the source channel goes above 50 BPM.

Control dialog and graph showing control channel detecting source channel levels less than 50 BPM
These examples are only a few of the possible applications of the control channel using the two threshold icons
on the left-hand side of the Control Setup dialog. You can construct variations of these (i.e., switching the
digital line from low to high using a wide threshold whenever the source channel drops below a given channel)
that are not discussed above. Moreover, each of the options can be construed somewhat differently than they
have been presented here. For example, the previous example switches the digital line from low to high each
time the signal on the source channel drops below 50 BPM. Conversely, it also switches from high to low each
time the source channel value is greater than 50 BPM. This allows you to vary the default setting for the digital
channels (whether the default is zero or +5 Volts) depending on what types of devices are connected.
(For a description of how to connect various digital devices, see the section on UIM100C connections in the MP
System) Hardware Guide.)
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Part C Analysis Functions 147
In addition to setting above and below type thresholds, you can program the Control channel such that the
digital line is switched whenever the source channel falls within a given range or outside a specified range. In
the example that follows, digital line 15 is set to switch from zero to +5 Volts whenever the source channel
signal falls between the values entered in the L1 and L2 boxes. In this case, I/O is switched to +5 Volts
whenever the heart rate is greater than 60 BPM but less than 80 BPM.

Control dialog and graph showing control channel switching from
low to high when source channel is between 60 BPM and 80 BPM
You can also program the digital line to switch from high to low when the signal on the source channel falls
within a given range. This is equivalent to setting the digital line to shift from low to high when the source
channel values fall outside a given range (as shown below).

Control dialog and graph showing control channel switching from
high to low when source channel is between 60 BPM and 80 BPM



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Fourier Linear Combiners: FLC, WFLC, CWFLC Calculations
Fourier Linear Combiners are linear combinations of adaptable sinusoidal functions that are particularly well
suited to processing cyclic data. Sine and cosine are harmonics that are multiples of a base frequency that are
summed together, and the order is the fixed number of harmonics used in the model. Step size provides mu, the
gain factor used to adjust the weights of the harmonics at each processing step. Step sizes must be much less
than 1 for the system to converge. As step sizes decrease, relaxation time lengthens. The FLC model is adjusted
based on the source data using least means square (LMS) feedback and the bias compensates for DC offset.
To have AcqKnowledge apply an FLC Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select FLC, WFLC, or CWFLC.
5. Click the Setup button in the Input Channels dialog to generate the appropriate dialog.
C See FLC Transform options, including Scaled FLC, on page 274.


Basic FLC
Simple summation of fixed
numbers of sines and cosines;
uses harmonics of a fixed
frequency and adjusts weighting
coeffiicients of the mixture.
Weighted-Frequency FLC
Base frequency of the harmonics
is variable; adapts the frequency
in response to the input signal
using LMS feedback; the
frequencies are similarly adjusted
to the amplitudes.
Coupled WFLC/FLC
Runs a WFLC on the signal to
determine the harmonic frequency
and then runs the result through an
FLC using the computed harmonic.
Operates on a single channel at a
time.
Operates on a single channel at a
time.
The second FLC can be run on the
same or a different channel.
Well suited for extracting data of
a known frequency band from a
signal with a stable frequency.
Use as an adaptive noise filter
to remove non-periodic and
semi-periodic noise
uncorrelated to the base
harmonic frequency.
Well suited for modeling periodic
signals of an unknown and
potentially varying frequency
and/or amplitude.
No cycle boundaries or
frequencies need to be pre-
determined.
Well suited for real-time extraction of
information from one signal based
upon the frequencies contained in
another signal.
Use to remove movement noise
from ECG.
Unique configurations can be
established with two input signals,
one for frequency and one for
amplitude.
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Part C Analysis Functions 149
Adaptive Filtering Calculation

C See the Adaptive Filtering transform on
page 271.
Adaptive filtering is a signal processing technique that
processes two different signals in relation to one another
and can be used for noise estimation, noise reduction,
general-purpose filtering, and signal separation. Adaptive
filtering creates efficient high-quality filters with a
minimal number of terms, which can be very useful in
blocking mains interferences or other known periodic
disturbances.
Useful for noise filtering where it is possible to
acquire a signal that is correlated to the noise (similar
to the way noise-cancelling headphones detect and
remove outside noise). Applications include removing
EMG from ECG or EOG from EEG.
To have AcqKnowledge apply an Adaptive Filtering Calculation in real time:
1. Choose MP> Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Adaptive Filtering.
5. Click the Setup button in the Input Channels dialog to generate the Adaptive Filtering dialog.
The weights within an adaptive filter are modified on a step-by-step basis. AcqKnowledge uses the N-tap FIR
adaptive filter, with coefficients updated using least means squares (gradient) feedback.
Order Specify a positive integer for the number of terms to be used in the internal FIR filter.
Step size Provides mu, the rate of adaptation of the coefficients within the FIR filter.
Source channel The source channel will be replaced by the adaptive filter results.
Noise channel The noise channel is the signal that is correlated with the noise to be eliminated from
the Source; it is not modified by adaptive filtering.
Source and Noise channels must have the same channel sampling rate (under Channel Set Up).


Comb Band Stop Filter Calculation
To have AcqKnowledge apply a Control Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Comb Band Stop.
5. Click the Setup button in the Input Channels dialog to generate the Comb Band Stop dialog.
See page 134 for details.

Metachannel
See Metchannel details on page 118.

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Rescale Calculation

Rescale applies two-point linear mapping and allows users to change the measurement units (for example, to
change temperature from Celsius to Fahrenheit). The text corresponding to the new units can be manually
entered.
To have AcqKnowledge apply a Rescale Calculation in real time:
1. Choose MP > Set Up Channels.
2. Click the Calculation tab.
3. Check an Acquire box for the Calculation channel you want to contain the filtered data. You may also
check the Plot and Values boxes as appropriate for each channel.
4. Click the Preset pull-down menu and select Rescale.
5. Click the Setup button in the Input Channels dialog to generate the Rescale dialog.

- Use the Rescale transformation (after acquisition) to adjust forgotten calibration of analog channels or
reverse incorrect calibrations.
- A "Rescale" Automator action has been added to allow rescaling to be performed in workflows.
The rescale formula is:


Rescale Source Displays the label and number of the selected channel.
Old Units Displays the values of the current vertical units of the channel
New Units Allows for manual entry of the new units to be used. The new units will be displayed in the
vertical units of the channel
Note When rescaling only a selected area of the waveform, the manual entry of new
units is not available unless Transform entire wave is checked since it is not
possible to display different units for different time ranges in the same channel.




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Part C Analysis Functions 151
Chapter 7 Set Up Acquisition

Set Up AcquisitionThe Basics
Once you have selected the channels to be acquired, the next step is to set up the acquisition parameters. These
options control the data collection rate, where data will be stored during an acquisition, and the duration of each
acquisition. Choose MP > Set Up Acquisition to generate the dialog to set these options.
Storage Mode
At the top of the dialog are three popup menus that allow you to control a number of aspects for storing the data
from each acquisition.
Record/Record last allows you to control whether the software saves all the data or only the most recent
segment of the data.
Recordthe hardware will store data for the amount of time that is specified in the acquisition length
box. This is the default and is appropriate for almost all types of acquisitions.
Record lastonly available when acquisitions are set to 'Save Once' or 'Memory'the hardware will
acquire data continuously, but will only store the most recent segment of data equivalent to the duration
in the acquisition length dialog. That is, if the value in the acquisition length box is 30 seconds and record
last is selected, the hardware will acquire data ad infinitum, but will only store the most recent 30 seconds
of the data.
Save once/Autosave file/Append allows you to vary how the data is saved to a file. By default, AcqKnowledge
will save the data to a single continuous file.
Save onceAcqKnowledge will begin an acquisition when the mouse is clicked on the start button, and
will stop either when the acquisition length has been reached or when the stop button is clicked with the
mouse.
Autosave file allows you to perform several acquisitions one after another, and save the data from each
acquisition in a separate file. When the Autosave option is selected, a File button will appear to the left of
the sample rate dialog. Click File to generate a standard Save dialog to enter the root file name for the
data from each acquisition. After you click Save in this dialog, another dialog is generated with options to
append an incrementing number, time (system clock), or date (system clock) to the filename: Media
functionality does not support the Autosave file acquisition mode.
Append similar to Save Once, except that Append allows you stop and restart acquisitions at
arbitrary intervals. Append mode is unique in that clicking on the Stop button only pauses the acquisition,
which can then be restarted by clicking on the Start button.
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In Append mode, each time an
acquisition is restarted, an append
event is inserted into the record
showing the time (hh:mm:ss) at which
the MP System (MP150 or MP36R)
started acquiring data. Although you
can pause for any period of time, the
MP System (MP150 or MP36R) will
only acquire data for the amount of
time indicated in the Acquisition
Length box. Data can be acquired in
Append mode while being saved to
memory, disk, or the MP data
acquisition unit (but not in Averaging
mode).

Sample data Acquired in Append mode.
Events indicate where Acquisition was paused.
Appended segments can be stored to disk, memory, or MP150. (MP36, BioHarness or B-Alert does not
support data storage to the hardware unit.)
Append to Disk: In this mode, it is usually best to record all channels at the same rate. If the user
stops the acquisition, the length will be the same for all channelsso the next segment of appended
data will neatly link onto the end of the existing record. If channels are sampled at different rates,
append to disk operation will cause the software to rewrite all data files in the graph and add extra
data to the uneven waves. This extra data will be a continuation of the same data point at the end of
each uneven wave. This operation may take some time to complete for very long data files.
You can append to existing filesjust open them, change the storage mode to Append to Disk
and Start the acquisition.
Append to disk requires AcqKnowledge 4 format files. If you open any other file format, you will
be prompted to translate the file.
Append to Memory: In this mode, data is appended to the uneven waves in the same manner as
described for Append to Disk. When channels are sampled at different rates, this mode will respond
faster than Append to Disk because the data files are already in memory so the software does not have
to rewrite all the data files in the graph.
A Reset button is generated in the Set Up Acquisition dialog when Append is selected. Click
the Reset button to erase the acquired data file and start a fresh acquisition file (this is
essentially the same as saying yes to an Overwrite existing data? prompt).


The Rewind button on the toolbar will delete the last recorded segment. Ctrl-Rewind (Windows) or
Option-Rewind (Mac OS X) will delete all recorded segments (similar to the Reset button).
Append plus external trigger
An acquisition that takes place over a long period of time with brief events which are few and far between can
be Set Up in the following manner: the researcher watches for these event, triggers the acquisition to start, and
then lets the pre-defined acquisition length run out. When another event of interest occurs, the researcher
triggers the next acquisition. This acquisition will be appended onto the end of the first acquisition.
Memory is the only limit as to how many appendages can be added.
Append plus Variable Sampling Rates
If the mode is started and stopped manually, it is statistically possible that, prior to the next pass of the
Append, extra data points may be inserted in various data channels to line up the data (see sample on page
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Part C Analysis Functions 153
109). These extra data points simply replicate the last sample in any affected channel. To minimize the impact
of the extra data points, make sure the lowest sampling rate is on the order of 10 Hz or higher, or dont use
VSR.
Disk/Memory/MP/Averaging determines where to store data during an acquisition. Once data has been
acquired and is stored in a file, it is stored on a hard disk or other similar device. There are a number of options
for storing data during an acquisition. The best choice as to where data should be stored during an acquisition
depends in large part on the nature of the acquisition itself, and the type of computer being used.
Memory stores data in computer memory (RAM) during an acquisition. After the acquisition is finished you
will have to select Save As... from the File menu to permanently save this to your computers hard disk.
This usually allows for faster acquisition rates, although most computers have less available RAM than disk
space.
Disk saves data directly to the computers hard disk during an acquisition. Disk mode is fast enough (in
terms of maximum sampling rate) for many applications, especially when only a few channels are being
acquired. Saving data to Disk also allows for longer acquisitions, since most computers have more hard disk
space free than free RAM. A final advantage of saving data directly to Disk is that if there is a system
failure (including power outage), all the data collected up to that point is saved on disk and can be
recovered, whereas the data is deleted if it is being saved to computer memory.
IMPORTANTWhen saving files to Disk, always be sure to save your files under a different name
BEFORE you start each acquisition. Otherwise, any previous data in that file will be overwritten.
In Memory mode, simply save the file after the acquisition.
MP stores a small amount of data on the MP data acquisition unit itself. The MP150 is limited only by
internal memory, with storage estimated at 4 MB and 400 kHz aggregate sampling rate.
Obviously, data cannot be sampled this fast for a very long period of time if it is to be stored in the MP data
acquisition unit. Also, as more and more channels are acquired, the duration of acquisition to the MP data
acquisition unit will shorten. Another drawback of storing data to the MP data acquisition unit is that the
data is not plotted on the screen as it is being acquired, but will automatically be plotted on the screen as
soon as the acquisition is terminated.
Averaging is used exclusively for acquisitions involving repeated trials; see page 157.
Acquisition Sample Rate
The value in the box labeled Sample rate indicates how many samples the MP System (MP150 or MP36R)
should take per channel during each second of data acquisition. The sample rate can be changed by clicking on
the pull-down menu. To allow for variable sample rates, the rate options are constrained so that channel sample
rates are equal to or a specific power of 2 less than the acquisition rate. Sample rates can be chosen at the
selected increments only; custom rates are not accepted.
Depending on the nature of the data being acquired, the best choice in terms of sampling rate will vary.
Technically speaking, the minimum sampling rate should be at least twice the highest frequency component of
interest. This means that if the phenomenon you are interested in observing has frequency components (which
are of interest) of 100 Hz, you should sample at least 200 times per second. Fourier analysis (FFT) can be used
to determine what frequency components are present in the data (see page 300 for a more detailed description of
the FFT function).
TIP: A good rule of thumb is to set the sampling rate to at least three to four times the highest
frequency component of interest.
In less technical terms, lower sampling rates can be used for data with slowly changing values (e.g. respiration,
EDA, GSR), whereas higher sampling rates should be set for data where values change markedly in magnitude
or direction (e.g. ECG, EEG, evoked response).
The maximum allowable sampling rate will automatically adjust itself according to the storage mode, how
many channels are being acquired in the channel setup window and the type of computer being used. You can
try this by entering a large value (say 99, 999) in the sample rate box. Now click the mouse button or press
return and AcqKnowledge will automatically return the maximum allowable sample rate given the computers
throughput and the acquisition parameters.
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If data is being stored to disk or computer memory (RAM) during an acquisition set to a sample rate that is too
high, the acquisition will begin normally, but AcqKnowledge will stop the acquisition and display a message
indicating that the acquisition buffer has overflowed. The data up to this point has been saved, and the sample
rate must be set to a smaller value if you wish to complete an entire acquisition.
The sample ECG waveforms below illustrate the effect of different sampling rates on obtaining varying levels
of fidelity when reproducing the data.
Top waveform: data is sampled relatively slowly; difficult to make out the shape of the waveform.
Middle waveform: sampled at the faster rate; more samples are taken in the same period of time, which
results in higher resolution for some components of the waveform.
Bottom waveform: sampled at a relatively high rate; increased resolution of the waveform. Waveform
components that were obscured at slow sampling rates are now well defined, and measurements taken on
this waveform would be able to better establish the maximum amplitude, time between different ECG
complexes, etc.


Representation of ECG waveform sampled
with relatively few samples per second
True ECG wave is superimposed over dots
that indicate sample points.

Preceding waveform as it would look if
plotted in AcqKnowledge (with data points
superimposed).




Representation of same ECG waveform
sampled at a relatively higher sampling rate.

As shown, under-sampling completely misses the QRS complex of this waveform, although it might detect
components of the QRS in subsequent beats. Although this is an extreme example of how under-sampling can
affect digitally processed data, it is important to note that the rate at which data is sampled has important
implications for the interpretation and analysis of data.
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Part C Analysis Functions 155


Acquisition length
To set the duration of an acquisition, enter a number in the acquisition length box. By default, 3600 seconds of
data will be recorded. The popup menu right of the length box allows you to scale the duration of the
acquisition in terms of milliseconds, seconds, minutes, hours, or samples. Changing this option will not change
the length of the acquisition, only the units used to describe it. Thus you can describe the same acquisition as
lasting 30 seconds, or 0.5 minutes, or 30, 000 milliseconds. Scaling the duration of an acquisition in terms of
samples is essentially the same as the time scaling options, except the length of the acquisition will be expressed
in the total number of samples to be collected on one channel.
Regardless of what scale you use to determine the length of acquisition, AcqKnowledge will end an acquisition
when the value in the total length box is reached. You may also stop the acquisition at any time by clicking on
the stop button in the lower right hand corner of the graph window.
The MP150 will automatically limit the maximum recording length to the amount of available memory on the
target storage device (memory, disk, or MP150). The default is to record one acquisition of the duration
specified in the acquisition length box. The acquisition length parameter has a somewhat different interpretation
in the Record Last and Averaging modes. See pages 151 and 157 (respectively) for more information on these
features.
Multiple Hardware
AcqKnowledge can be used with multiple data acquisition units to:
Control multiple, independent experiments on one computer
Increase the total number of channels used for a single experiment (e.g., 32-channel EEG)
To synchronize the Start of multiple units, use the External Trigger function.
To combine nearly unlimited channels of data into one file, use the Merge Graphs feature (see page 259).
Each graph window can
support a different MP unit. To
add an MP unit for acquisition,
open a New Graph (not a Data
View).
To show/hide the Connected
to: information, toggle the
Show/Hide Hardware icon in
the Toolbar.

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156 AcqKnowledge 4 Software Guide
To switch the hardware unit
associated with a graph
window, click the Connect
to box and select an available
unit or choose Add New
Device. Different hardware
types may be added and
consolidated in the list by
selecting Add New Device.
Choose No Hardware to run
AcqKnowledge in analysis
mode only.
The Choose MP150 dialog
shows the MP150 units
residing on a local network.
(Network functionality is
limited to MP150 hardware
only.)
Click the Help button to
open a troubleshooting guide
(PDF) with support tips to try
if an MP150 is not
communicating with the
computer.

NOTE: When switching to a BioHarness BT device from another hardware
type, a new graph must be launched in order for the BioHarness settings to
take effect. (File > New > Graph Window)


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Part C Analysis Functions 157
Averaging
Overview
In some instances, the signal of interest does not stand out against the background or ambient noise (the level of
ambient noise exceeds the signal produced by the object of interest), and the only way to detect the signal of
interest is to perform repeated trials as part of one acquisition, and average the trials together. Since the noise
associated with the signal is assumed to be random, and the signal is assumed to be systematic, the noise
should approach zero as the individual trials are averaged together.

Signal (top) measured in the presence of noise
(middle), which results in the bottom waveform
when measured in standard Acquisition mode

Same signal averaged in the presence of noise
over 2,000 trials to produce the lower waveform.

Any averaging acquisition consists of three general components:
(a) the stimulus signal
(b) the duration of the acquired data, and
(c) a small amount of processing time (or overhead) that takes place between acquisitions.
The duration of the stimulus signal and the duration of data to be acquired can be set by the user. The amount of
overhead required is a function of the acquisition length, the sampling rate, and the number of channels being
averaged.
Acquisition length
Stimulus signal
Overhead
Latency

Stimulus signal usually some sort of pure tone or pulse; occurs at the beginning of each trial.
Acquisition length refers to the amount of data to be acquired during each trial.
Overhead refers to a period of time after data has been acquired that is needed to
perform the mathematical averaging.
Latency refers to the total time elapsed between the start of one trial and the start of
the subsequent trial.
Important usage notes
The maximum length of a single averaging pass is restricted to 2 seconds; if longer averaging passes
are required, use regular data acquisition and use the Ensemble Average offline analysis option to
generate averages in post-processing.
The preferred hardware setup for on-line averaging mode is direct connection to the MP150 via
cross-over cable. To improve stability, avoid interruptions during acquisition:
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158 AcqKnowledge 4 Software Guide
- Do not access top-level menus (File, Edit, Transform, etc.) or generate popup dialogs (Setup).
- Avoid running other programshelps ensure that required system resources (processor time,
memory, and network throughput) remain available.
- If the MP150 is connected over a network, avoid running applications that consume network traffic
(Internet Explorer, mail client, media player)these may interrupt/delay communication to the MP150.
Averaging Setup
For Advanced Averaging, see page 160
To set up Averaging:
1. Choose MP150 > Set Up Acquisition
and select using Averaging option.
2. Click the Setup button to generate
the Averaging options dialog.
3. Set the Averaging options as detailed
below.
4. Click OK to close out of the dialog.
5. Set the Stimulus (see page 168).
6. Use the buttons in the graph window
to Start, Stop, and save the averaging
acquisition.
Online averaging progress bar
An online averaging progress bar is a toolbar
that is added to graph windows in
AcqKnowledge 4 when online averaging
acquisitions are in progress. The toolbar
displays the number of averaging passes that
have been completed and the number of
passes that have been rejected by the MP150
firmware. This is similar to the text displayed
in the status area of Windows AcqKnowledge
3.9.1 and earlier.


Averaging Options
Averages
Select the number of averages to perform from the pull-down menu, to a maximum of 10,000.
Latency
The individual components of stimulus signal, acquisition length, and overhead are, in sum, equal to the latency
of the acquisition. As a rule, you should set the latency to at least three times the acquisition length. In some
casessuch as when you want to allow a subject to return to a baseline state or conditionyou may want to set
the latency to a value much larger than this. By default, each trial is initiated when the latency value is reached
(in the sample dialog shown, a new trial is initiated every 100 msec).
If the latency is set to a value too short to allow for averaging to take place, an Acquisition Warning will be
generated:

Adj Latency: automatically adjust the latency
to the shortest possible value that still allows
for data to be acquired and processed.
Adj Length: reduce the amount of data
acquired without changing the latency.
Abort: return to the graph window without any
data being collected.

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Part C Analysis Functions 159
Averaging Options continued

External trigger
To initiate a trial on a signal from an External Trigger, enable this option and select positive or negative edge.
When this option is checked, a new trial will be acquired each time a trigger circuit is closed. For more
information on triggers, see page 165.

Artifact rejection
Occasionally during an acquisition, extreme levels of artifact will be present for one reason or another.
Checking artifact rejection allows you to determine what signal levels constitute artifact, and have the MP
System reject these trials. When artifact rejection is enabled, the MP System (MP150 or MP36R) will ignore
any trials that contain signals exceeding the artifact rejection thresholds, keep track of how many trials have
been rejected, and add that number of trials to the total number of trials to be acquired. This allows you to re-
try a trial that was rejected due to the presence of artifact.
To set these parameters, you need to set a high threshold and a low threshold. Both thresholds refer to the scale
limits (normally 10 Volts). If the high and low artifact rejection thresholds are set to 80% and 30%
(respectively), the MP System will reject any trial where the signal exceeds +8 Volts or 3 Volts.
When the channel scaling feature is used to change the range of Map (Scale) values to something other than 10
Volts, the artifact rejection formula for symmetrical limits is: y = ((2PV)/100)x PV
where y = voltage threshold
PV = Peak Value
x = percent threshold (whole number)
If non-symmetrical limits are used, the following equation is used: y = ((V1-V2)/100)x + V2
where y = voltage threshold
V1 = Higher Peak Value
V2 = Lower Peak Value
x = percent threshold (whole number)
Enable Channels
To add analog channels to the average, check
additional channels in the Enable list.
Channels must be set to Acquire under
MP150 > Set Up Channels to be selectable
here; otherwise the channel box will be
grayed out.



Stimulus Signal
Although AcqKnowledge does not require a stimulus signal to be output for Averaging trials, most applications
that use signal averaging make use of a stimulus signal. Digital stimuli (i.e., clicks) or analog stimuli (i.e., tones,
pulses, and arbitrary waveforms) may be output.
In almost all cases, the most convenient way to output a stimulus signal is to output a predefined wave on
analog output channel A0 and/or A1. You can create pulse waveforms, tone waveforms, ramp waveforms, and
arbitrarily shaped analog waveforms. Use MP150 menu > Stimulator Setup to set all of the stimulus output
functions (see page 168).
When you start Averaging, the Start button turns to Averaging status and the green dot turns to A to indicate
that Averaging is in process.
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Advanced AveragingP300
Advanced averaging can be used to set up P300 protocols. A sample P300 setup is included in the Samples
folder.
To set up Advanced Averaging:
1. Open two or more graph files.
2. Use Set up Acquisition to set each graph file for Averaging (see page 157).
3. Click the Averaging Setup button and set Averaging Options as desired for each graph file.
Advanced Averaging will use the defaults if you choose not to set Averaging Options for
Latency, Artifact Rejection, or Enabled channels.
4. Use Setup Stimulator to establish the desired stimulus output for each graph file (see page 168).
Set the Output channel to the same channel (A1 or A0) for all graph files.
Set the Stimulator Output to During Averaging Pass (recommended).
5. Save each graph file with an appropriate name.
6. Choose MP150 > Set Up Advanced Averaging.

This menu option is only enabled if two or more open
graphs are set to Averaging.

7. Set the Advanced Averaging options:

a. Averages: Select the number of averages from the pull-
down menu (max 10,000).
b. Graph: Assign a Graph from the pull-down menu of open
graph files. Up to eight graph files can be used in
Advanced Averaging.
c. Trial distribution: Use the slider to assign a percentage for
each graph; the total will adjust to 100%
Note The software counts 0 as 1, so the percentage of the
active graph should be entered as one less than the
desired output (for 50% enter 49%).
8. Click the Start button in the Advanced Averaging setup dialog to begin acquisition.
9. Review the status in the Completed bar that is activated when Start is pressed and/or in the status
display at the bottom of the AcqKnowledge software window.


10. Save each graph file.
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Part C Analysis Functions 161
11. Make sure that the Graph names are correct in the Advanced Averaging setup dialog, and then use Save
or Save As to save the setup as an AVG file.


Repeating
The Repeat mode allows you to acquire data from repeated trials using the same parameters for each trial.
Checking the Repeat every box at the bottom of the acquisition setup dialog enables a series of dialogs and
popup menus at the bottom of the dialog. These allow you to control how many times an acquisition will repeat
as well as the interval between trials. When this is unchecked, the acquisitions will repeat as soon as possible
(usually instantaneously, but slightly longer if data must be saved to a file between trials).

Interval The entry to the right of the Repeat every checkbox tells AcqKnowledge how long to pause
between the start of one acquisition and the beginning of the next acquisition. This can be scaled in
terms of seconds, minutes, or hours using the second popup menu.
It is important to note that this value measures the interval between the start of two adjacent trials,
rather than the interval between the end of one trial and the start of the subsequent trial. If the repeat
interval is set for 15 minutes and the acquisition length is set to 60 seconds, then there will be a 14-
minute pause between the end of the one trial and the beginning of the next.
Trials Set how many trials to acquire:
for perform a finite number of trials; enter the number of trials to acquire
forever perform an infinite number of trials. Trials will be repeated at the specified interval until
the acquisition is stopped either by clicking on the stop button in the graph window or if
there is not enough free memory on the target storage device.
Regardless of which options are checked, data for each trial is acquired according to the acquisition parameters
specified in the dialog. In the above example, each trial of data will be sampled at 50 Hz and will last 1 minute;
the trials will be repeated every 15 minutes for a total of 8 trials.
By default, each acquisition will delete the data from the previous acquisition. You can change this by selecting
the Autosave file option from the Save once/Autosave file/Append option at the top of the acquisition setup
dialog. When the repeating option is checked and Autosave is selected, AcqKnowledge will save the data from
each trial using the file name and extension indicated by the autosave feature. See page 151 for a more detailed
description of Autosave.
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Setup Channel Options
Channel The Channel column contains the alpha-numeric channel numbers. Analog (or
continuous) input channels begin with CH and run from CH1-CH4. Digital input
channels begin with D and run from D1-D8. Calculation channels begin with C
and run from C1-C12.
Display is limited to four channels of each type. Use the scroll button to set up
additional Digital or Calculation channels.
Acquire When the Acquire Data box is checked for a given channel, data will be collected on
that channel.
Plot If Plot on Screen is also checked, data will be plotted on screen in real-time during the
acquisition. If the plot box is unchecked, data will still be recorded for that channel, but
the waveform display will be disabled. To display the waveform plot after the acquisition
is over, show the channel.
Enable Value
Display
Checking the Enable Value Display box means that you can choose to display
(numerically and/or graphically) the values for each channel in real time. To display the
values, you must also select Show Input Values (via the MP36 menu). Input values are
displayed in a separate window from the main graph window.

Default The default is to collect one channel of data on analog channel 1 (CH1), and to plot and
enable value display for this channel
TIP Usually, you will want to check all three boxes for each channel you acquire data on
Label The Label entry for each channel allows you to type in up to 38 characters to identify the
channel.
Presets

Clicking on the Presets button will generate a menu of available presets for the channel.
Presets for common applications configure the hardware gain, filters, etc.
For a detailed summary of Analog Input channel, Digital Input channel, and
Calculation channel options see the Presets section beginning on page 117.
View/Change

To View/Change Parameters for a Preset, click the wrench icon. If you change the
parameters, you have the option of creating a New Channel Preset to make the
established parameters available to other channels.
If you make a change to a preset and start recording in the Append mode, you will be prompted as follows.
Choose Abort, save your data, and then change the presets to acquire as a new data file.

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Part C Analysis Functions 163
Starting an acquisition
After setting up the channels and defining the acquisition parameters, you are ready to start the acquisition. If a
file window is not already open, choose File > New to generate a graph window.
In the lower corner of the screen, next to the button, you should see a button with a circle to the left
of it. The circle indicates the status of the communication link between your computer and the hardware. If the
unit is properly connected to the computer and is turned on, the circle should be solid and green. If the unit is
not properly connected, a solid gray circle will appear (on monochrome displays, the circle will appear solid
when the MP unit is connected properly, and unfilled when the unit is not communicating with the computer).
You can start the acquisition by positioning the cursor over the

button and clicking the mouse button
or by selecting Ctrl + Spacebar. If there are no input devices (e.g., electrodes or transducers) connected to
the hardware, it will collect a small value of random signal noise with a mean of about 0.0 Volts.
For information on how to connect measurement devices to the MP36R, see the BSL Hardware Guide.
You may also start an acquisition using a variety of triggers, which are discussed on page 165.
Once acquisition starts, the button in the acquisition window changes to . The two
opposing arrows to the right of the button indicate that data is being collected. Also, the Busy status indicator
light on the front of the MP150/MP36R will illuminate, showing that data is being collected.

Stopping an Acquisition
To stop an acquisition at any time, click the button in the lower right corner of the screen or select
Ctrl + Spacebar. An acquisition will stop automatically when it has recorded an amount of data equal to the
Acquisition Length entry.

Rewind
The Rewind button on the Toolbar allows you to erase the last recorded data segment and continue to
Append data to the existing data file. This function will erase the last segment along with the Append Event
for that segment; the application will keep track of Append Event labels, so that the label always matches the
segment number.

If the Warn on Overwrite option is active, a warning dialog will be generated before the segment is deleted.

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Saving acquisition data
To save a data file, pull-down the File menu and choose the Save command.

Electrode Checker


The Electrode Checker, in conjunction with the MP36R unit, measures how well electrodes are making
contact with the surface of the skin. To use this feature:
1) Attach the electrodes as you normally would.
2) Connect the electrodes to an electrode lead set (such as the SS2LB).
3) Instead of connecting the electrodes to one of the four analog inputs, connect the Simple Sensor end
of the electrode lead to the Electrode Check port on the front of the MP36R acquisition unit.
4) Click the MP36 menu and scroll down to select Electrode Checker.
This will generate a small thermometer-like display. At the bottom of the display you should see a number
with kO after it. This value describes the impedance of the electrode/skin contact, with lower numbers being
associated with better conductivity. The better the conductivity, the cleaner the signal displayed on the screen.
If the MP36R is off or no nothing is connected to the Electrode Checker on the MP36R unit, the Electrode
Checker display will say OFF.

Poor contact Good contact Off
TIP While there are few absolutes as to what constitutes good contact, one rule of thumb is that this
number should be below 10 kO, and the lower the better.
TIP To decrease the impedance of an electrode connection, you may want to abrade the surface of the
skin with an abrasive pad (such as ELPAD). This removes a thin layer of dead skin cells and
should result in a signal that has relatively little noise.

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Part C Analysis Functions 165
Chapter 8 Set Up Triggering
During a normal acquisition, the MP System (MP150 or MP36R) will begin collecting data following a mouse
click the start button. It is also possible to begin acquisition using a trigger. Using a trigger allows you to start
an acquisition on cue from a variety of different trigger sources. All trigger options are set in the Set Up
Triggering dialog, which can be selected from the MP menu. By default, the trigger is Off, and acquisitions are
started by clicking on the Start button in the graph window. Other options can be selected from the popup menu
in the Triggering Setup dialog. To begin an acquisition with a trigger, first choose the trigger options most
appropriate for your application and then click the Start button. After the Start button has been pressed, data will
be acquired as soon as the trigger is activated. There are two general types of trigger sources: digital channels
and analog channels.

Digital Triggers
Digital channels are channels that contain binary
(either/or) data as typified by a switch being either open or
closed. This type of data can be acquired from a push-
button switch or other device that produces an on/off
pulse. For instance, it is sometimes useful to have an
acquisition begin when a subject presses a button or when
a signal generator sends out a pulse. These are typical
digital signals and the trigger devices that emit these
signals can be connected via the UIM100C. Most stimulus
generators are equipped to output a digital pulse
simultaneously with the stimulus signal.
In a simple trigger design, an external switch is connected
to the TRIG and GND D input as shown above. Since this
switch will be either open or closed, the data will be
digital and have two levels, +5 Volts and 0 Volts. A value
of +5 Volts is interpreted as a binary 1, and a level of 0
Volts is interpreted as a binary 0. In the setup above, when
the switch is closed (i.e., the button is pressed) the signal
changed from +5 Volts to 0 Volts, creating a transition or
edge.
If the trigger is set to external, and the edge is set to
positive, the acquisition will begin as soon as the push-
button is pressed anytime after the start button in the graph
window is pressed. Once the button is pressed, the
acquisition will proceed according to the acquisition
parameters you have set (acquisition length, sampling rate,
and the like).
BIOPAC
Systems
GND A
+12 V
-12 V
8
9
10
11
12
13
14
15
TRIG
+5 V
GND D
1
2
3
4
5
6
7
0
Pushbutton
switch

0 Volts 0 Volts
+5 Volts
Positive
edge edge
Negative
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Analog Triggers
Initiate an acquisition when an analog channel reaches a certain level. To enable the analog trigger feature, data
must be acquired to either memory (RAM) or disk, and a value must be entered in the Delay box (although the
delay may be set to zero). The channel containing the data to be used as a trigger does not require the
acquire/plot/values boxes to be checked in the Set Up Channels dialog. Leaving these boxes unchecked will
allow the incoming data to trigger an acquisition but will not cause the trigger channel to be acquired or plotted.
Select MP > Set Up Trigger to generate the Trigger dialog:



Source Off: Disables Triggering while maintaining the established setup.
External: Select for Digital Trigger.
CH #: Select for Analog Trigger; must be acquiring to Memory or Disk. Specify the analog
channel that contains the trigger data and then specify a voltage Level to initiate the trigger.
Acquisition will begin when the data on the specified channel reaches the specified Level.
To trigger an acquisition when an ECG wave on analog channel 1 reaches a certain voltage
or value, you would set Source to CH 1 and then set the Level when the entry box is
enabled.
Triggering from an analog channel requires oversampling by a factor of 4, which ensures
that the trigger signal will not be missed. The sampling rate can be adjusted in the Set up
Acquisition dialog.
o For example, an initial sampling rate of 1,000 samples/second should be increased to
4,000.
Level The Level option is activated when a Source CH is selected. Set a level to initiate the trigger (e.g.,
if the ECG wave peaks at 3 V, set the trigger level just under 3 V).
Edge Triggers can have a positive or negative edge, defined as follows:
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Part C Analysis Functions 167
Edge Digital Analog
Pos signal changes from 0 to 1 signal crosses from a baseline to a peak
Neg signal changes from 1 to 0 signal crosses from a peak to a baseline
For ECG data (and other types of data with peaks of relatively short duration) there will be
only minor differences between the two edges, although the positive and negative edges
can be widely separated in time for data with slowly changing values (such as GSR or skin
temperature data).
Mode Once the trigger channel and level have been specified, the final parameter is the delay. Delay can
be measured in terms of samples, milliseconds, seconds, or minutes, and may be set to zero if
desired. The delay option instructs the MP System to wait a specified period after the trigger level
is reached before beginning the acquisition.
Delay When using a trigger, the default setting is for the acquisition to begin immediately after the
trigger pulse or level occurs. You can change the default by using the Delay option in the Trigger
Setup dialog. This feature allows an acquisition to begin a specified period after the trigger level is
reached. If you want to start an acquisition one second after a switch closes, set the trigger to
external and enter 1.00 in the box next to Delay. The default scale for Delay is seconds, meaning
that the acquisition will begin a specified number of seconds after the trigger has been initiated.
The scale of the delay can be changed from seconds to samples, milliseconds, or minutes.
Pretrigger During normal triggered acquisitions, data is collected only after the trigger has been activated (or
after some delay). For some applications, it is useful to collect data on events that occur just prior
to the trigger event. As an example, if an acquisition was set to begin when a device (such as a
tone generator or flash) sends an output pulse, it might also be important to collect information on
the subjects state just before the stimulus.
Pretrigger functionality is not supported in all acquisition modes (MP150 > Set Up Acquisition):
Mode Source: EXTERNAL Source: CH #
Disk Pretrigger supported Pretrigger supported
Memory Pretrigger supported Pretrigger supported
MP150 Pretrigger supported not available
Averaging not available not available
When the Pretrigger function is enabled, start an acquisition by clicking the Start button. When the
internal memory in the MP data acquisition unit is full, the MP System (MP150 or MP36R) will
start replacing the oldest data with the newest data (similar to the record last feature). This process
continues until the trigger event occurs. Following the trigger, the MP System (MP150 or MP36R)
will collect data until the total length is reached. The acquisition now contains data from both
before and after the trigger.
The amount of data collected before the trigger event is determined by the value in the box next to
the Pretrigger popup menu. As with Delay, scaling can be set in terms of samples, milliseconds,
seconds, or minutes. The duration of the Pretrigger may also be adjusted using the scroll box to the
right of the Pretrigger dialog.
When Pretrigger is selected, it is important to note
The total length of the acquisition includes the duration of the Pretrigger. If the acquisition
length is set to 120 seconds and the Pretrigger is set to 20 seconds, only 100 seconds of data
will be collected after the trigger event occurs.
Since the total length of the acquisition includes the duration of the Pretrigger, the duration of
the Pretrigger may not exceed the length of the acquisition.
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Chapter 9 Set Up Stimulator

Although data acquisition is the primary function of
the MP System, you may also output a signal
through one or two analog channels while data is
being acquired. This is handled through a window
similar to the standard AcqKnowledge graph
window.
Four types of signals can be output:
1. Square waveformspage 174
2. Tone waveforms175
3. Ramp waveforms175
4. Arbitrary waveforms176
Each of these waveform types can be set to repeat
signal output either Once or Continuously, and
parameters can be set to either Relative or Absolute
time scales.

To set the type of waveform to be output, select Setup stimulator from the MP150 menu. This generates a
window that allows you to control the type of signal output by the MP System. Like the standard graph window,
this plots time on the horizontal axis and amplitude on the vertical axis.
You can use this window to create and shape waveforms to be output. Adjust the Stimulator Sample Rate
(described below) to further control the parameters of the Stimulator Output design.
For any waveform (or stimulus) to be output, you need to specify the type of stimulus, the shape of the signal,
the output channel to be used, and how many times the stimulus should be output.
All of these parameters can be set from within the Stimulator Setup dialog. Regardless of the type of waveform
you select, stimulus signals will normally be output when an acquisition is initiated, either as a result of clicking
on the start button or a trigger being activated.
Stimulator Sample Rate
A very powerful feature intrinsic to the MP150 unit is the ability to set a stimulation signal output rate that is
different than the acquisition rate, thus permitting considerable flexibility for a variety of physiological
applications.
Use the pull-down menu to select a unique sample rate for the stimulator.

See also: Application Note AH162 - Using the Stimulation Features of the MP System.
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Part C Analysis Functions 169
Parameters
Reset Refresh the display; use after the time scale has been adjusted.
Scaling Scaling buttonRescale stimulus signals to units other
than Volts according to the Change Scaling Parameters.
This type of rescaling does not change the amplification of the
signal, it is useful for recalibrating the output signal to more
meaningful units. In the example shown here, an output signal of +10
Volts is rescaled to +128 dB, while an output signal of 10 Volts is
rescaled to reflect 0 dB.

Relative Set the duration of each segment of the output waveform in Seg # Width. In the sample dialog
shown below left, a 5000 msec output is created by entering individual segment widths: 500 + 400 +
250 +200 + 3650 = 5000 msec



Output
A# Analog Output You can output on one or two analog output channels. The output channels are listed
as A0 and A1 and correspond to Analog Output 0 and Analog Output 1 the UIM100C.
For dual stimulation and independent control, connect an output device to A0 and A1.
See Analog Output for MP150 Users notes on page 172.
The maximum resolution of a stimulus signal output through an analog channel is 22 sec; this means
that the shortest segment in the stimulus signal must be at least 22 long.
PW Pulse Width AcqKnowledge allows you to output a single digital pulse through digital channel I/O 15,
with a resolution of 1 sec. Since this is a true digital channel, pulse output has only two levels (0
Volts and +5 Volts), which cannot be edited. The segment that can be edited is the pulse width
(duration), which can be set to any value greater than 1 sec.
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Duration:
Set independently for A0 and A1.

Off: Turn Output OFF (no stimulus signal output).
Output once: Output the stimulus signal once.
Output continuously: Output the stimulus signal for the duration of the acquisition (forever).
When output continuously is selected, a vertical line
is generated at the end of the first section of the
waveform in the stimulator window to indicate where
the first output signal ends and the second begins.
The line can be dragged left or right like a vertical
segment in a stimulus waveform to control the
duration of the waveform as it is continuously output.


Use to choose the sample rate for the generated signal.


Control timing of output by aligning it with the Start button, waiting until a trigger is initiated before generating
the signal, or manually toggle the selected stimulator on or off. Click the lock button to synchronize both
stimulator outputs to the On/Off buttons.
NOTE: Wait until trigger option is only active if Triggering is enabled in the MP150 menu.
Trigger
When a trigger option is selected (in the Trigger Setup window), AcqKnowledge allows you to select from
additional options with respect to when the signal is output. By default, the stimulus signal will be output
when you click the start button. When a trigger is enabled, however, you have the option of either
outputting the signal when the start button is pressed or when the trigger is initiated. The trigger option is
added to the stimulator window when a trigger is enabled in the Setup Trigger box (described on page
165).
Manual Stimulator Control
Only available when a stimulator is connected and with MP150 units running firmware 1.1.14
or higher
When an MP150 unit is being used, the manual stimulator controls at the bottom of the Stimulator Setup
dialog can be used to start and stop stimulators independently of the acquisition. If changes are made to the
stimulus wave while a stimulator is running, the stimulator will need to be turned off and then back on to
apply the changes to the settings.
The manual stimulator controls can not be used if the MP150 is set to acquire in averaging mode.
- Acquisition will start the stimulator when the acquisition starts.
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Part C Analysis Functions 171
- On/Off button will start the stimulator when the Start button in the Stimulator Setup
window is engaged. The Start button toggles to a Stop button.
If Dual Stimulator settings are active, Start with applies to both stimulators.
A lock between the two sets of controls can be used to turn both stimulators on or off at
the same time. This lock is useful for two-channel stimuli delivery, such as stereo sound.
UNLOCKED

LOCKEDBoth channels Start/Stop together

Stimulator Output Type

If an averaging acquisition is selected in the MP setup, the timing can be set to delay the averaging pass until
after the signal is generated, or to include the signal output in the averaging pass. Note that the signals cannot
exceed the duration of the averaging pass.
The Digital setting will generate a true digital pulse (0 Volts and +5 Volts) prior to the averaging pass on
digital I/O Channel 15.
For Averaging details, see page 157.

Finish all output, then start averaging pass Include output in averaging pass

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Analog Output for MP150 Users
The two MP150 Analog Output channels can independently output static or dynamic values:
- Static output: Use Manual Control (page 219) to set the output level for each channel in the
range -10V to +10V.
- Dynamic output: Use Stimulator Setup (page 168) to define the output level and pattern.

The MP150 will automatically use the Manual Control value if:
- No acquisition is in progress OR
- Acquisition is in progress but the Stimulator is disabled via the Setup Stimulator dialog.

The MP150 will only use the Stimulator Setup value if:
- Acquisition is in progress (or before Averaging pass) AND
- Stimulator is enabled via the Stimulator Setup dialog.

When the stimulator is in use:
1. Any Stimulator Output starts (from before Time = 0) with the value established for Manual
Control.
2. If Segment # Width = 0 the stimulator ignores the associated Segment # Level.
3. If the stimulator is in 1x mode, after the output waveform is sent, the value of the last segment is
fixed until acquisition stops.
4. When acquisition stops, the stimulator resets to the Manual Control value.

The following dialogs and output illustrations demonstrate how the Manual Control value influences
Analog Output for the Stimulator when an MP150 is used:

Acquisition parameters:





Stimulator parameters:








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Part C Analysis Functions 173
Manual Control list box: Stimulator Output pattern (using MP150):


Dual Stimulation
For independent control of two stimuli (such as sound and electrical output), set stimulator functions for Output
to A0 and A1 for each MP150 unit. Click the tab for each output at the top of the Stimulator Setup dialog and
complete independent settings.


For additional stimulus paradigms, add MP150 units (see Multiple Hardware, page 155).


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Square waves
Square waveforms are useful for generating
pulse waveforms, which can be used as stimuli or
to trigger a stimulus-generating device (such as a
flash device or a tone generator).
To output a square wave, choose the Output
Once in the Duration section. You should see
a rectangular wave appear in the window. You
can control the shape of the wave by
manipulating the various segments of the wave.
A square wave has five segments, and
AcqKnowledge allows you to set the level
(amplitude) and width (duration) of each
segment.
In a square wave, each of the editable segments is oriented horizontally, with vertical segments connecting the
adjacent sections of the wave. The first segment of a pulse waveform is the segment that appears at the far left
of the waveform section. By positioning the cursor on this segment of the waveform, you can tell from the box
at the bottom of the screen that the level (vertical offset) of the first segment is 0 Volts, and the width of the first
segment is 500 msec.
To adjust the level of a segment, either:
a) enter the desired level in the box that says Seg # Level; or
b) position the cursor on the first segment of the waveform and drag it up or down using the mouse
(segment 2 is selected in the preceding dialog, and appears in red).
To change the duration of a segment, either:
a) Enter a value in the Seg # Width box at the bottom of the Stimulator Setup dialog; or
b) Position the cursor on the first vertical segment in the setup dialog, click the mouse button, and drag the
vertical segment left or right. Moving the first vertical segment left shortens the duration of the first
segment, whereas moving the first vertical segment right lengthens it.
Each of the segments in the pulse wave can be edited in this way.
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Part C Analysis Functions 175
Tone Stimuli
Tone waveforms allow you to create pure tone
signals of any duration, magnitude, and frequency. This
option outputs a pure sine wave, which is useful for
audiological and stimulus response testing.
A tone waveform is comprised of two segments, with
only the second segment being the actual tone itself. This
allows you to include a pre-signal delay (by setting the
level for Segment #1 to 0 Volts and the duration to a
desired value).
To set the duration of the tone, adjust the length of
segment #2 (by changing the Seg #2 Width value box or
by clicking and dragging the segments within the
window). As shown, there is an additional (uneditable)
section of the waveform after the second section. This
segment returns the last value from segment two, and
continues to output that signal level until the acquisition
is terminated (if the stimulator is set to output once) or
until another signal is output (if the MP System is set to
output continuously).
There are three additional parameters for Tone waveforms: frequency; magnitude; and tone phase.
Tone frequency refers to the frequency of the second segment of the waveform. This can be set to any
value, although the most common settings are between 20 Hz and 20,000 Hz.
Magnitude refers to the peak-to-peak range of the signal, which can range from 0 to 10 Volts.
Phase of the stimulus signal can be any value equal to or greater than 0 degrees. Phase settings of more
than 359 degrees will be rescaled to fit the 0-359 range. In other words, setting the phase to 360 or
720 has the same effect as setting the phase to zero degrees.

Ramp Waves
Ramp waveforms are useful when you need to
construct a monotonically increasing or decreasing
stimulus signal. Ramp waves are comprised of three
segments and the amplitude and duration can be set for
all three sections.


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Arbitrary Waveform
The Arbitrary waveform option allows you to set a
waveforms shape and length using standard
AcqKnowledge editing functions.
The length of an arbitrary waveform is only
limited by the available memory.
Unlike the other types of waveforms, Arbitrary
waveforms have no segments, so the shape
of the waveform is determined by selecting an
existing waveform and the only parameters
that can be set are Scaling, Repeats, and
Trigger.
There are two methods to create an arbitrary waveform:
A. Copy waveform segment
1. Open a waveform in a standard graph window.
2. Select the section of the waveform you wish to
output.

3. Return to the Stimulator Setup dialogthe
selected area will automatically be pasted into
the dialog.
B. Create waveform
You can also construct an Arbitrary waveform by copying and pasting predefined stimulus waveforms
(e.g., square waves or ramp waves) into a standard graph window. This is useful when a pure signal needs
to be modified by adding noise or modifying waveform parameters such as rise time or decay. It also
allows you to combine complex sequences of existing stimulus waveforms, such as a pulse followed by a
tone.
1. Create a waveform in the Stimulator setup (as described above) of the desired duration and shape.
2. Choose Edit > Copy.
3. Switch to an empty graph window.
4. Choose either Insert waveform or Paste from the Edit menu.
5. Modify the waveform characteristics as desired.
6. Choose Edit > Copy.
7. Switch to the original graph window and paste into the Stimulator Setup window.
8. Output as an arbitrary waveform.
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Part C Analysis Functions 177

Stimulator Icons
Waveforms:

Square wave


Tone (sine) wave


Ramp wave


Arbitrary wave
Parameters:

Reset the display (use after adjusting the time scale)


Scaling (rescale Stimulus signals to different units)


Set time base to relative
Output:

Tab to output to Analog Output channel 0 (default)


Tab to output to Analog Output channel 1






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Chapter 10 Output Control
Note: Output Control chapter refers to MP36R hardware only.
For MP150, see the previous chapter, Set Up Stimulator.
The MP UNIT can output pulses or analog voltages via the Analog Out port; this
port is also used to connect to BIOPACs external stimulators. The MP36R has an
additional I/O Port which is used to output digital (TTL Level) signals.
Parameters for output signals are set via Output Control. Access to a specific
Output Control is via the MP36R > Output Control submenu.
There are seven Output Controls for the MP36R:
Output Control See MP36R Functionality
CH# to Output page 180 Direct analog CH1-4 to output listen to signals



Digital Outputs page 182 Control 8 digital outputs
Pulses page 186 Use with third-party devices; software can control pulse width and
repetition.
Stimulator - BSLSTM page 183 Use with BSL Stimulator
Low Voltage Stimulator page 183 MP36R: Use OUT3 adapter for MP36R built-in low voltage
stimulator. Software can control pulse amplitude, width and
repetition (-10 to +10 V)
Pulse Sequence Page 188 Direct analog CH1-4 output. Allows for output of customized
pulse trains.
Sound Sequence Page 187 Outputs customized sounds assignable to a user configurable pulse
train.
To open an Output Control, select it from the MP UNIT > Output Control submenu. A checkmark appears
next to the submenu selection and an Output Control panel is displayed, bordered in red in the active data
window. To close an Output Control, select from the menu again (toggles between display and hide) or right-
click in the open control panel and choose Close.
Only one Output Control panel may be open at any time. Switching between different data files can change the
display and operation of the control panel.
Because some output devices can be used for stimulation on humans and can achieve voltages up to 100 Volts,
built-in software logic makes output control as safe as possible.
See page 200 for safety notes regarding human subjects.
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Part C Analysis Functions 179
The following applies to all Output Controls.
The output will not operate unless its software control panel is open.
When an Output Control panel is closed, or the AcqKnowledge application is closed, MP36R output goes to 0
Volts, preventing the output device from sending pulses.
When an Output Control panel is opened, output is always OFF until activated by a click of the ON/OFF switch
in the control panel or, if parameters allow, a click of the Start button in the data acquisition window.
(Exceptions are the Voltage Output Control, which outputs immediately, and the Digital Outputs Control when
set to the preference Set each output immediately.)
Output preference parameters are local and are saved with the data file or a graph template file. The data or
template file holds the output parameters as established when the file was saved. (See Save as Graph
Template, page 237.) Switching between other open graphs can change the display and operation of the control
panel since the settings in each graph are independent entities.
If desired, custom Output preference parameters can be saved as a preset for a current graph (file preset) or for
all graphs (global preset) by using the Save Settings button in the Output Preferences window. A saved
Output preference can be recalled by choosing Organize List and selecting the desired custom preset.
CH to Output
Use both the Output Control panel and its respective Preferences dialog to control the output signal. Output
Control Preferences dialogs establish the parameters for output. Preferences dialogs are only available when
the corresponding Output Control panel is open and active.
To generate the Preferences dialog, either:
Open an Output Control panel and then right-click anywhere in it to
generate a pop-up menu. Choose Preferences to open the dialog (Close
will close the control panel).
or
Open an Output Control panel
and then choose File >
Preferences and select from
the submenu to open the
dialog.

If a control panel entry box is grayed or disabled, its values may be established, or limited, by settings in the
Preferences dialog. If Preferences parameters allow, enter values directly in the Output Control panel.

Key into the entry boxes and then enter the value by pressing the Enter key.
Use the Tab key or mouse to move to another entry box.
Click the OK button if in the preference dialog.
Values entered into a control panel or its Preferences dialog that are outside the specifications of the output
device, or outside the limits defined by the Preferences dialog, may change automatically to reflect either the
closest value to that requested that the hardware can achieve, or the closest increment defined by the limits in
Preferences. (The system will not check while you type, it checks and may make changes after the value is
entered.)
For example, if a Pulse width of 5 ms is entered into the Pulses Output Control panel entry box, but Preferences
defines a range limit of .5 to 2 ms for Pulse width, the system will automatically change the new entry to 2 ms.
Saving Panel settings:
Output Control panel settings will be retained until a file is closed or saved. If a file is closed but not saved,
settings will be lost (defaults established); if a file is saved, panel settings will be saved.
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CH# to Output Output Control

The CH# to Output Output Control redirects an analog input signal to the Analog Out port on the back of the
MP UNIT. The signal from the assigned channel will continue to be recorded and plotted as it normally would.
This Output Control is used mainly when attaching headphones to the MP UNIT to listen to signals coming in
on an analog input channel. One common use is listening to the EMG (muscle) signal, a clinical procedure
physicians use to actually hear certain problems with muscles.
To display this control panel:
Choose MP UNIT > Output Control > CH# to Output to open the control panel.
MP36R users may use analog input CH1-CH4. Channel 3 is the default setting. If another channel N has been
designated, the menu will read CH<N > .
Use the control panel ON/OFF Switch to start and stop output. OFF grounds the output so no signal (or sound)
should be present.
Preferences
Set Preferences to designate which channel to redirect to output.
Open the Preferences dialog (right-click in the control panel or choose File > Preferences > CH# to Output).
Use the pull-down menu to select the desired channel CH 1-4 to use for the output.
Click OK to set the output channel and return to the control panel.
Note Only the Hardware settings (Gain, Offset, Input Coupling)
from the Input Channel Parameters dialog (MP36R > Set up
Channels > Wrench) will be applied since output is established
prior to the processing of Digital Filters.
See MP36R Input > Output Scaling values on the next page.


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Part C Analysis Functions 181
MP36R Input > Output Scaling
The MP36R hardware can pipe signals from any channel input to the output using the CHX to Output control
panel in the AcqKnowledge softwaredue to the difference between the input and output range, there will be a
change in signal level (scaling). The output range depends on the output pin used as shown in the following
table.
Output Pin
(Analog Out port)
Pin Description Output Range
(Volts)
Pin 1
Headphones,
A.C. Coupled
-2.048 to +2.048
Pin 2
Low Voltage Stimulator,
D.C. Coupled
-10 to +10
The input range is gain-dependent. The table below shows the scaling (multiplying) factors to use for each gain
setting.
Output Scale**accurate to 10%
Factor 1 Factor 2
Gain Input Range
+- millivolts
Pin 1 (Headphone out) Pin 2 (Low Voltage
Stimulator)
x5 2 V 1.024 5
x10 1 V 2.048 10
x20 500 mV 4.095 20
x50 200 mV 10.238 50
x100 100 mV 20.475 100
x200 50 mV 40.950 200
x500 20 mV 102.375 500
x1,000 10 mV 204.750 1,000
x2,000 5 mV 409.500 2,000
x5,000 2 mV 1023.750 5,000
x10.000 1 mV 2047.500 10,000
x20,000 0.5 mV 4095.000 20,000
x50,000 0.2 mV 10238.000 50,000
Notes
* 1: To properly measure the output signal you need at least a 2K Ohm load.
** 2. Input to Output scaling is accurate to within 10%.
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Digital Outputs Control


The Digital Outputs Control allows control of signal output on each of eight digital lines via the I/O Port
connector on the back of the MP36R. Use it to control external devices. The digital output uses standard TTL
levels which correspond to the control panel setting as follows:
Control Panel setting Output Voltage level (Volts)
0 0
1 +5
To display this control panel:
Choose MP36R > Output Control > Digital Outputs to open the Digital Outputs Control panel
Click each digital output line to set its digital state to 0 (off) or 1 (on).
If desired, you may set Preferences for Digital Outputs.
Open the Preferences dialog (right-click in the control panel
or choose File > Preferences > Digital Outputs).
Select from the following two options:
Set each output immediately (default) allows you to toggle the state of each digital output line between 0 and
1, and change the state immediately. In this mode, no Set button is available in the control panel. Output for
each line is set upon clicking its toggle button.
Set all outputs when Set button is pressed allows you to toggle the state of each digital output line, but the
states will not physically be changed until the Set button is clicked on the control panel. In this mode, a Set
button is available in the control panel. When the Set button is clicked, all eight digital lines will update
simultaneously.
Click OK to set Preferences and return to the control panel.
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Part C Analysis Functions 183
Pulses Output Control
Stimulator BSLSTM Output Control
Stimulator Low Voltage Output Control
Control panel options for Pulses, Stimulator BSLSTM and Stimulator Low Voltage

Additional control panel options for Low Voltage Stimulator
A variety of pulse output options are available. Exercise caution when using any of the options with human
subjectssee the Safety Note on page 200.
Pulses Output Control
Select this Output Control for general pulse output, or when synchronizing to 3
rd
-party devices.
Use for reaction time measurements, where a subject listens with headphones for a series of clicks (pulses)
and responds as quickly as possible with a button press. Determine reaction times by calculating the time
between the start of the pulses and the responses.
Use with the BIOPAC STP30W Stimulus Presentation System (SuperLab) to measure responses to visual or
auditory stimuli. To perform sophisticated evoked response averaging tests (e.g. P300), pair triggers with
different visual or auditory stimuli.
Use to trigger another device (automatically send a pulse from the MP UNIT when acquisition starts).
Use to control a 3
rd
-party stimulator. BIOPAC recommends use of the BIOPAC BSLSTM Stimulator with the
MP UNIT and BIOPAC software. If using the BSLSTM Stimulator, use the Stimulator - BSLSTM Output
Control instead of this Pulses Output Control.
Stimulator BSLSTM
Select this Output Control when using the Biopac Student Lab stimulator
(BSLSTM)
Use with stimulation electrode HSTM01 for safe stimulation of human
subjects (0 100 Volts), as well as lower voltage (0 - +10 Volt) general-
purpose stimulation, such is used with amphibian muscle or nerve
preparations.

Set up note Placing the BSLSTMA/B unit too close to MP UNIT hardware can result in data distortion of the
BSLSTMA/B pulse width signal; distortion is more apparent at higher sampling rates.
- NEVER set the BSLSTMA/B atop an MP UNIT
- Position the BSLSTMA/B away from the MP UNIT to reduce the signal distortion
Low Voltage Stimulator
Select this Output Control for low-voltage (-10 - +10 Volt), direct drive
stimulation via MP36RAnalog Out port (with or without OUT3 BNC
adapter).
Use with stimulator electrode HSTM01for safe, stimulation of human subjects (0 100 Volts), as well as lower
voltage (0 - +10 Volt) general-purpose stimulation, such is used with amphibian muscle or nerve preparations.
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Outputs through a BNC connector so it can be used
with most stimulation cables (such as those that
terminate in a needle probe).
To use one of these control panels:
Choose MP UNIT > Output Control and then select Pulses, Stimulator BSLSTM, or Low Voltage Stimulator.
Control panel options for Pulses, Stimulator BSLSTM and Stimulator Low Voltage

Additional control panel options for Low Voltage Stimulator


Right-click in the Output Control panel (or choose File > Preferences and select from the sub-menu) to
generate the Output Preferences dialog.

Set the Preferences.
General: ON/OFF, Number of pulses, Event options see page 191


Advanced: Pulse width, Pulse repetition (rate) see page 194
Level (low voltage only): Pulse level see page 197
Reference Channel (low voltage only): Channel assignment, signal generation Once configured, Preferences
may be saved using the Save Settings command, activated by pressing the button at the bottom of the
Preferences dialog (see page 191).
Confirm the settings in the control panel. Adjust as desired within the parameters established in Preferences.
Entry limits: Settings entered into the Preferences dialog may establish, or limit, the values in the Output
Control panel entry boxes. You may enter pulse settings directly into the control panel only if parameters
established in Stimulator Preferences allow. If an entry box is grayed or disabled, its value is set or limited by
Preferences.
Initiate the pulse sequence as defined in Preferences (see page 191).
ON/OFF Button in Output Control Panel uses the switch in the Control panel.
Recording uses the Start /Stop button in the data acquisition window.

To close an Output Control panel:
Right-click anywhere in the Output Control panel to generate a pop-up menu and then choose Close, or select it
(or another output control) from the MP UNIT > Output Control submenu.

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Part C Analysis Functions 185
Pulse Sequence Output Control
In AcqKnowledge 4.2 and higher, this Output Control allows sequences of pulse configurations and delays to be
sent to the MP36R unit, making it possible to create more complex stimulus setups.

Enabling the pulse sequence output control option will display the following control panel at the top of the
graph window:


Pulse sequence configuration is performed in the Preferences dialog of this output control panel. (Accessible via
right-click on panel shown above or from FilePreferences) When a pulse train element is selected in the
configuration, the controls will become visible in the right hand portion of the preferences dialog. The
configuration makes use of three basic building blocks:

A sequence consisting of a number of delay and pulse train elements. The final configuration consists of one or
more sequences that are outputted in order. Normally the entire configuration is outputted. There is a special
operational mode on Start with Recording that will take only the indexed sequence matching the current
recording segment.

A pulse train element consisting of a fixed number of pulses of identical width output at a
fixed pulse frequency.

A delay element that allows for the introduction of time during which no pulses will be generated.

Each one of these building blocks also has a repeat count associated with it that will perform the action a set
number of times. (Adjust by selecting the desired Repeat and inputting a new value) Individual sequences,
pulse trains and delays can be added, repeated and reordered as desired. In the right pane of the Preference
dialog (shown below), fixed or random pulse counts, widths and repetitions can be configured and combined.
As in other Output Controls, custom settings can be saved and organized in a list view. (See below for
additional setup dialogs)

For a full explanation of preferences and tabs common to all Output Control panels, see the Output Control
section on page 190.


Preferences available in Pulse Sequence tab
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Preferences available in Options tab


Delay Preferences

About Delay between Pulse Trains:
The amount of actual Delay between pulse trains will vary from the set value depending upon the pulse
repetition value that is used. In the example sequence below, a Delay of 100 milliseconds between pulse trains
has been set up, combined with a pulse repetition rate of 20 milliseconds. Because the pulse repetition rate is
applied before the Delay occurs, the actual Delay between pulse trains in this case will be 120 milliseconds. If it
is critical that a Delay reflect an exact value, it is advisable to subtract the selected pulse repetition value when
setting up the Delay parameters.

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Part C Analysis Functions 187

Delay between pulse trains
Sound Sequence Output Control
In AcqKnowledge 4.2 and higher, Sound Sequence Output Control offers users the option of configuring and
customizing sounds to be outputted for aural stimulus experiments. The control panel and Preferences dialogs
used for Sound Sequence closely resemble that of Pulse Sequence. The built-in sound resource (a default
click) may be used or any other file in *.WAV format can be substituted via the File and Browse button.
The Width and Pulse Repetition values are dependent upon the duration of the sound file selected for
output. The Test button will output an audio sample of the selected sound resource.



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The option all sequences means that each configured sound sequence (regardless of number) will be outputted
within the same segment. If "Once" is selected in the "Output entire pulse sequence" option, a configured
sequence will be heard one time only. If "Continuously" is selected, the first Sound Sequence will be repeated
after the last one has completed, looping the pattern repeatedly until the recording is stopped.

The option each sequence means that each sound sequence will be outputted on a segment-by segment-basis
only. For example, if one Sound Sequence is configured, it will only be heard during the first recording
segment, but not during the second recording segment). If two Sound Sequences are set up, the first one will be
heard during the first segment and the second one during the following segment. If no additional Sound
Sequences have been configured, nothing will be heard during the third segments and beyond. (Exception: If
"Save Once" acquisition mode is used, the Sound Sequence will be repeated when the recording is overwritten
during subsequent passes).

The following terms are used in the Output Control panels, Preferences, and guidelines for Pulses, Stimulator
BSLSTM and Low Voltage Stimulator.
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Part C Analysis Functions 189

Delay before first
Pulse
Initial delay from start of acquisition to start of first pulse.
Number of pulses Number of successive pulses that will be sent out at the specified Pulse Width,
Repetition and Level. Set for Single (1), Multiple, or Continuous (Cont).
Pulse Level Amplitude of the pulse, expressed in Volts.
Note: The output of the BSLSTM is 0 Volts when the pulse is not active.
Pulse Repetition
Also called
Events per second
Pulse frequency Pulse
sequence
Pulse train
Repetition rate
Sample train
Can be expressed as Period (ms) or Rate (Hz).
Period: Time between pulses; measured in milliseconds from the start of one pulse to
the start of the next pulse.
Rate: Number of pulses that occur in a one-second interval; measured in Hertz.
Rate relates to Period as: Rate (Hz) = 1000 / Period (ms)
Pulse Width Time that the pulse is in the non-zero or active state.
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Output Control Panel Descriptions
The Output Control panels for Pulses, Stimulator BSLSTM and Low Voltage Stimulator work in conjunction
with Preferences to control pulse output. Control panel functions are detailed here:
OUTPUT CONTROL PANELS
General Notes
Pulse parameters can interact with each other.
For example, the pulse repetition period cannot be set to a value less than the pulse
width.
In order to simplify the interaction, the Pulse width entry overrides other entries as
required; it is the priority parameter.
For example, if the pulse width is changed such that it exceeds the pulse repetition
period, the pulse repetition period will be automatically adjusted to
accommodate the new pulse width entry. If, however, the pulse repetition period
is changed such that it is less than the pulse width, the repetition period will be
changed, upon attempted entry, to the closest value that can be achieved without
changing the pulse width.
Entries are checked and rounded (not truncated) as necessary to meet limitations of
the hardware or the Preferences.
When a file is opened, the output device will not turn ON automatically. A user must
manually press either the Record button or the Start button.
The exceptions are the Voltage Output control panel and the Digital Outputs
control panel if Set each Output immediately is selected; these settings will
output values immediately.
Output control settings are local, which means that they are stored at the data file
level, not the program level. Use the save as graph template (File > Save As) option
to use existing Preferences in new data files.
If a file is saved with an Output Control panel visible and then closed, the panel will
be visible when that file is re-opened.
Preferences
Right-click a control panel to generate the Preferences dialog, and then select a tab
for the settings you want to adjust.

You can also use the File > Preferences menu option to generate the Preferences
dialog.
Output Settings


Displays the name of the current Preferences setting. The pull-down menu lists the
names of all output Preferences saved using the Save Settings button (see page 191).
The pull-down menu is not accessible when an output pulse train is in progress.
If no settings configurations have yet been saved, when the Output Control panel is
first opened and no parameters are changed, the Output Settings box displays
Default. If any parameters are changed (but not yet saved), it displays Custom.
When output settings are saved, the Output Settings box displays the name of the last
selected setting. Use Organize List to change the display order of the menu, rename,
or delete items (see page 191).
When a saved setting is selected from the pull-down menu, the Output Control panel
and all Preferences dialog options will be updated.
For Reference ChannelLow Voltage only: All Output Settings must use the same
reference channel assignment; other parameters can be unique for each setting.

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Part C Analysis Functions 191
OUTPUT CONTROL PANELS


Once configured, Preferences may be saved using the Save Settings button at the
bottom of the Preferences dialog. Save Settings generates a dialog to name and save
a defined configuration of Stimulator output settings. Saved configurations are
accessible via the Output Settings pull-down menu in the Output Control panel.
When a setting is selected from the menu, all current output parameters are updated
to reflect the saved settings.
You can save multiple configurations as long as each has a unique name; the Save
button will be inactive if the name you enter is not unique.
Output settings configurations are local presets that are saved with the data file or a
template file. The data file or template file holds the output parameters as established
when the file was saved plus any other named configurations of Output Settings.


Use the Organize List button at the bottom of the Preferences dialog to order,
rename or delete saved Preferences settings. The up or down arrows are only
available if two or more settings have been saved. Select a setting and then click the
up and down arrows to set the position, or choose rename or delete. If you choose
Delete All, all saved settings will be deleted and the default and Custom options
will be reactivated.

GENERAL TAB (OUTPUT PREFERENCES)
General Tab

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GENERAL TAB (OUTPUT PREFERENCES)

Number of Pulses

Indicates the number of pulses to be output. When the Output Control panel is
closed, the pulse output will be immediately stopped.
Single will establish a single pulse for outputting. All pulse repetition options, entry
boxes and scroll bars in both the control panel and preferences windows will be
disabled (grayed).
Multiple will establish a specific number of pulses for outputting. The selection will
activate an entry box where you can enter 1-254 pulses. When this option is selected,
the Pulse Repetition scroll bar is activated in the Output Control panel.
Continuous will establish a continuous pulse train for outputting. When this option
is selected, the Pulse Repetition scroll bar is activated in the Output Control panel.

MP30 Only If using High Speed mode ( > 2,000 s/s) and Initiate pulse sequence
with Recording is selected, the stimulator cannot be turned off manually since the
MP30 will not accept any commands from the computer until the recording has
stopped.
If Initiate pulse sequence with ON/OFF button in Output control panel is
set, the pulse sequence will be stopped prior to acquisition and will have to be
manually turned back on after the recording.
Initiate pulse
sequence with
ON/OFF Button

OFF (red)


ON (green)


AUTOMATIC
START (yellow)

Controls the start and stop of pulses. Changes to Pulse Width and Repetition Rate
can be made in the Output Control panel entry boxes during a pulse sequence, and
during a recording, if all other Preferences parameters allow it. Any change in the
pulse output will occur immediately. This lets you change the stimulator output on
the fly.

When Initiate pulse sequence with ON/OFF button is selected:
The ON/OFF button controls pulse output independent of the acquisition status.
OFF is always available.
The ON/OFF button reflects the current output state, with one exception: if the pulse
sequence lasts less than 0.5 seconds, the button will remain in the ON state for
at least 0.5 seconds to indicate that the ON state occurred.
When the Number of Pulses selected is Multiple, ON/OFF acts as a momentary
switch. Press the ON (green) button to start pulses;
it will automatically turn OFF (red) at the end of the specified pulse train.
The switch defaults to OFF. Saving a data file or saving as a Graph Template will
save all stimulator preferences except the status of the pulse switch, which will
always be saved in the OFF position.
Recording

Start button


Stop button
When Initiate pulse sequence with Recording is selected:
If the preference setting Initiate pulse sequence with: ON/OFF button is active, the
control panel changes will take effect immediately. If settings are changed during a
pulse train, changes do not take effect until the next time the stimulator starts.
Pulse output turns ON and OFF corresponding to the Start and Stop of the recording.
In other words, the Pulse output can only occur during a recording.
When in this mode, and not recording, the ON button will display as yellow,
indicating that pulse output will automatically begin at the Start of the recording.
Pulse outputting can be turned OFF during a recording, but it cannot be turned back
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Part C Analysis Functions 193
GENERAL TAB (OUTPUT PREFERENCES)
ON until the end of the recording.
When a Repeat sequence is running, pressing the OFF button will turn OFF the
output for the entire recording sequence and the button will display as OFF until after
the last sequence, when the switch will display as yellow ON (automatic start)
indicating that pulse output will begin again at the Start of the next recording
sequence. You cannot turn pulse outputting back ON during a repeated recording
sequence.
When the acquisition stops, all stimulator pulses will cease, regardless of the Output
Control panel settings.
The pulse train will stop concurrent with the end of the acquisition, even if the
specified pulse train is not completed before the acquisition ends. When a new
acquisition is started, the pulse train will start from the beginning.
In this mode, no changes can be made in the Output Control panel until the recording
stops. Changes made after recording stops will take effect when a new recording
is started.
When a pulse is sent out, the event label and indicator arrow will be generated (if the
event preference is turned ON and events are displayed).
After initial delay After initial delay of is enabled only when Initiate pulse sequence with
Recording is chosen. Specify a delay interval from the start of recording to the start
of the first pulse. This is useful for viewing data prior to the stimulus pulse. The
BIOPAC output device determines the delay range.
INITIAL PULSE DELAY MP36R or BSLSTM
Range 0 - 100 milliseconds 0 or .5 - 100 milliseconds*
Resolution 10 microseconds 1.953 microseconds
*Entries greater than 0 milliseconds must be at least 0.5 milliseconds.
Pulse Events


An advantage of using the AcqKnowledge software for output signals is that
information regarding the pulse is automatically recorded along with the data. On
most chart recorders, information regarding the pulse level (amplitude), pulse rate,
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GENERAL TAB (OUTPUT PREFERENCES)
and pulse width must be noted by hand, a process that can be inefficient, time-
consuming and error-ridden.
The amplitude reflects the output pulse level.
Eventscan be automatically inserted and labeled for each Reference pulse or
change in pulse train. The label will contain the Pulse width and Pulse rate (and
system time stamp if selected).
Events reflect setting changes made during an acquisition.
All output pulse information is automatically recorded and archived with the
saved data.
Set the event option by clicking in the box to Create event when output is changed.
Set the time stamp option on the global Event Preferences tab.

The event label accurately captures pulse data, but the event arrow may not always
line up exactly with the leading edge of the pulse; this typically is not a problem
because the recording will include the actual stimulus pulse which can be used for
timing measurements.
Depending on the acquisition Sample Rate, the leading edge of the pulse in the
recording may not correspond to the exact time the pulse was sentit may be off by
as much as one sample period. If the event precision is critical for your recording,
increase the Sample Rate.
To display events, use the toolbar icon or Display > Show > Events.
The Range switch on the front of the BSLSTM stimulator should be set to 10V or
100V prior to recording and should not be changed during recording; if using a
Preset, the corresponding Preset should also be selected prior to recording. The pulse
level can then be determined by moving the decimal to the right or left depending on
how the range was switched.
ADVANCED TAB (OUTPUT PREFERENCES)
Advanced Tab

Pulse Width
Indicates the Pulse Width setting, which determines the maximum Pulse Rate
frequency. You may enter a Pulse Width value, unless limited by Preferences.
The entry is activated when the value is changed and the Tab or Enter key is pressed;

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Part C Analysis Functions 195
GENERAL TAB (OUTPUT PREFERENCES)

it does not require a stimulator restart to take effect.
The Pulse width entry overrides other entries as required; it is the priority parameter.
An entry may be automatically changed if any of the following conditions apply, in
which case the closest possible value will be selected:
It falls outside the allowable range.
It is rounded to .01 millisecond increments (MP36R resolution).
Width has been limited by the Pulse Width: Limit Entry settings of Preferences.
Allow any entry
Pulse width is limited to the output capabilities of the BIOPAC MP device. This
option allows any entry within the allowable range specified below:
PULSE WIDTH RANGE MP36R unit
Range .050 100 milliseconds
Resolution 10 microseconds
Lock entry to
This entry locks the width to a single, specified value (within the allowable range). No
other value can be entered.
Pulse Repetition

Indicates the Pulse Repetition period (Hz or ms).
The Pulse period must be greater than the Pulse width. See TBPMIN in the
Output Preference > Advanced Tab Limits table on the next page.
The full range of acceptable Pulse Rate values is from .2 to 6,667 Hz (MP36R) or .2
to 6,827 Hz (MP30).
The maximum Pulse rate (PRPMAX) depends on the Pulse width setting:
Pulse width 100 ms maximum Pulse rate = 9 Hz
Pulse width .020 ms maximum Pulse rate = 3333 Hz
The formula for pulse width vs. pulse repetition is PRPMIN = PW + TBPMIN
Where: PRPMIN = the MINimum Pulse Repetition Period allowed.
PW = Pulse Width setting
TBPMIN = MINinum Time (in ms) between successive pulses
for the output device (see device specifications)
If Limit changes from ___ to ____ is selected in Advanced preferences, then
PRPMAX will be determined by the formula above or the specified limit, whichever
is greater.
An entry may be automatically changed:
If it falls outside the allowable range.
To round it to .01 Hz increments (resolution of system).
To make it at least 0.1 millisecond greater than the Pulse width.
By the Pulse Repetition Rate: Limit entry Preference.
By the Pulse Repetition: Adjust entry increments Preference.
You may manually enter any value for pulse width, but when using the scroll bar or
arrows, entries will be constrained by the Adjust entry increments Preference
setting.
Pulse Repetition The Pulse Repetition Scroll Bar adjusts rate or period by the increment of change and
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Scroll Bar limits established in Preferences. With each click of the scroll bar arrows, the rate will
be increase by the specified increment.
When Initiate pulse sequence with ON/OFF button in Control Panel is selected,
changes take effect upon release of the scroll box as long as the stimulator is running.
The scroll bar is disabled when Number of Pulses is set to Single or Pulse
Repetition is set to Lock Entry to...
Display as Pulse repetition can be displayed as
Pulse Rate (expressed in Hz), or
Pulse Period (inverse of Pulse Rate, expressed in milliseconds).
Pulse Repetition Rate relates to the Pulse Repetition Period as:
Pulse Rate (Hz) = 1000 / Pulse Period (milliseconds)
The Display as units selection is also used for:
Pulse repetition entries in the control panel.
Scroll bar increments.
The Pulse Repetition Rate: Limit entry Preference.
The Pulse Repetition: Lock entry Preference.
The Pulse Repetition: Adjust entry increments Preference.
When units are changed from Rate in Hertz (Hz) or Period in milliseconds (ms), the limits
of the Pulse Repetition range will be converted by the formula:
Period increment in ms = Round to nearest whole number [Period Range * (Rate
increment in Hz /Rate Range in Hz)]
For example, if the Range was 1Hz to 10 Hz with an adjustment increment of 1Hz,
the proportional calculation would be Period increment = 900 ms (1Hz / 9 Hz) = 100
ms
Allow any entry
Pulse width is limited to support the output capabilities of the BIOPAC output device.
See Output Preference > Advanced Tab Limits table for allowable range.
Limit entry Establishes minimum and maximum values that can be manually entered or changed
with the scroll bar.
Lock entry
Locks the Repetition to a single, specified value (within the allowable range). No
other value can be entered in the control panel.
Adjust entry Controls the scroll bar or scroll arrow increment; does not apply to manual entry.


Advanced Tab Limits Pulses BSLSTM
Pulse width
Range (ms):
.050 100 .049 100 .050 100 .049 100
Resolution (ms):
.010 .001953 .010 .001953
Pulse Repetition

Rate range (Hz):
.2 16,667 .2 10,204 .2 - 2,000 .2 2,004
Period range (ms)
.060 5,000 .098 - 5,000 .500 5,000 .499 5,000
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Part C Analysis Functions 197

TBPMIN Minimum time
between Pulses (ms):
.010 .049 .450 .450
Resolution (ms):
.010 .001953 .010 .001953
Initial Pulse Delay

Time range (ms):
0 100 0 or .5 - 100 0 100 0 or .5 - 100
Resolution (ms):
.010 .001953 .010 .001953

LEVEL TAB (OUTPUT PREFERENCES)
About Level

The Low Voltage Stimulator allows the software to specify the pulse amplitude.
The amplitude can be set to any value within the limits of the stimulator; the range
is -10 to +10 Volts.
Pulse Level
Low Voltage only

The Level entry box allows the user to
manually enter any value within the limits
of the system or within the limits of the
Preference settings from the Level tab.

The Level entry box will be inactive
(grayed) if:
The Level preference Lock entry to is
active.
If Initiate pulse sequence with Recording is active (from the General tab) and a
pulse sequence is in progress or wait for trigger is in progress.
Use the entry box or the scroll bar to set the Pulse level. When a value is entered
which is out of range, the value will be rounded to the closest value obtainable
after the Enter or Tab key is pressed.
If Initiate pulse sequence with ON/OFF button in control panel is active (from
the General tab), then values entered during a pulse sequence will take place
immediately.
If Initiate pulse sequence with Recording is active (from the General tab), any
entry made between acquisitions will take place on the next Start of acquisition.
Allow any entry The level is limited from -10 to +10 V to support the output capabilities of the
stimulator. This option allows any entry within that range.
Limit entry This entry reduces the range (within the -10 to +10 V range limit).
Lock entry This entry locks the level to a single specified value (between -10 and +10 V).
Adjust entry This setting affects the scroll bar or scroll arrow increment only; it does not apply
to manual entry.
The smallest increment is 5 mV, as limited by the MP36R. The specified
increment is used to round manual entries to the closest obtainable value.
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LEVEL TAB (OUTPUT PREFERENCES)
Reference Channel
SS58L only


This option allows you to Monitor the output signal on one of the analog or
digital input channels without making any physical connections. This is an
internal, hardware/firmware, feature that recreates the output signal and allows
recording in real time. The assigned reference channel will override any real
input signal.
For example, if a transducer is connected to CH 1, and CH1 is chosen as the
reference channel, then the signal coming from the transducer will not be
viewable, and will not conflict with the reference signal generated internally.
The reference signal is not the real signal, but is a very accurate estimate of the
real signal. The pulse timing accuracy will be within 100 microseconds. If an
analog input channel is used as the reference channel, the pulse level will be
accurate within 5%. If the SS58L encounters a load that reduces or distorts the
pulse output, the reference signal will not reflect this amplitude distortion.
If a digital input channel is used as the reference channel, only a digital
representation of the pulse will be generated. In other word, regardless of the
pulse level, when no pulse is occurring, the level will be 0 Volts, and when the
pulse is occurring, its level will be shown as +5 Volts.
Channel Assignment Use the pull-down menu to choose which analog or digital input channel will be
used as the output reference channel.
When a new reference channel is assigned, a warning will be generated to alert
you that this setting will overwrite the existing Channel Setup parameters for the
selected channel.

For example, if you set up CH1 for ECG data and then select CH1 for the
Reference Channel, your ECG parameters will be replaced. If you then select
another channel, CH1 will be reestablished with the default analog input
parameters, and you would need to recreate your ECG settings (by using Presets
or manual entry).
The reference Channel label should read: Low Voltage Stimulator - Reference
Out.
When an Analog Input Channel is assigned as the Reference channel, that
channel, as viewed from the MP UNIT > Set up Channels dialog, will be in a
Lock-Out mode. This means that the Preset pull-down menu icon for that
channel will be grayed (inactive). The assigned reference channel will be inactive
for real inputs until the Reference Channel Preference is changed to None or
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Part C Analysis Functions 199
LEVEL TAB (OUTPUT PREFERENCES)
another channel. The wrench button, when pressed for the Reference channel, will
still allow viewing of the channel parameters, but all entry boxes and pull-down
menus will be inactive.
When a Low Voltage Stimulator control panel using an assigned Reference
channel is closed, the channel that was assigned as the reference channel will be
removed from Lock-Out and will automatically change to the default, CH X
Input settings. The reference channel assignment will be saved in the template or
data file, so that if the Low Voltage Stimulator control panel is reopened, the
reference channel will be automatically re-assigned, without any warning prompt
given.
Generate using You can specify how the Reference signal should be shown.
If using analog input from CH1 - CH4, you may select actual or fixed (max)
amplitude and actual pulse or fixed pulse width. Fixed pulse widths are useful
when the pulse width is much smaller than the sample interval (1/sample rate)
being used.
For example, for Frog muscle stimulation, you may choose to use a 1 ms pulse
width, but a sample rate of 200 samples/sec. to capture the muscle response. At
this sample rate, the stimulus pulse could not be reliably recorded. By extending
the displayed pulse width to 100 ms, you will be guaranteed to always record the
stimulus pulse.
If using digital input from D1 - D8, select actual or fixed (15ms) pulse width.

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Usage Guidelines & Setup Summary for BSLSTM Output Control
HUMAN SUBJECT SAFETY
Before using the stimulator on human subjects, it is very important to limit the energy
the stimulator outputs. For optimal safety:
Before powering on the BSLSTM stimulator, set the voltage level to zero by rotating
the LEVEL knob on the front of the BSLSTM fully counterclockwise.
Use BIOPAC HSTM Series Probes. You MUST use these probes order to limit the
energy the stimulator can output.
Never create an electrical path across the heart.
Never use on subjects with pacemakers.
Read this manual and the BSL Hardware Guide to become familiar with Stimulator
operation.
Connect the BSLSTM Stimulator to the MP UNIT and power on both units. (For instructions on how to connect
the BSLSTM to the MP UNIT Acquisition Unit, refer to the BSL Hardware Guide.)
Connect the Stimulator Trigger cable to the Analog Out port of the back of the MP UNIT.
Connect the Stimulator Reference Output cable to an Input Channel on the front of the MP UNIT. This channel
will be set up in Step 3 as the Stimulator Reference Channel.
The Reference pulse has a fixed Pulse width of 15 milliseconds, so chosen so that the Sample Rate of the
recording may be as low as 100 samples/second and still capture the Reference pulse.
Before powering on the BSLSTM stimulator, set the voltage level to zero by rotating the LEVEL knob on the
front of the BSLSTM counterclockwise all the way to the left.
Launch AcqKnowledge software to a new data acquisition window.
Confirm that Events are activated.
Events are activated by default. If not activated for a given recording, choose Display > Show > Events.
Set up the Stimulator Reference Channel. This is the Analog
Input Channel on the front of the MP UNIT that receives the
Stimulator Reference Output cable from the back of the
BSLSTM.
Choose MP UNIT > Set up Channels. This will generate a Set up
Channels dialog.
Select the Acquire, Plot and Enable options for the analog
channel to be set up as the Stimulator Reference Channel.
Click Presets and scroll to select Stimulator (0-10V) or
Stimulator (0-100V) to match the Range switch setting on front
of the BSLSTM.
Click View/Change Parameters. This will generate an Input
Channel Parameters dialog.
Read the entire Stimulator section of this manual and familiarize yourself with the unit and its options before
changing any preset parameters.
You may set the Gain and other input parameters as desired.
Click OK to accept the parameters.
Close the Set up Channels window.
Adjust the voltage output of the stimulator by using the Level control on the front of the BSLSTM.
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Part C Analysis Functions 201
Rotate the Level knob clockwise to increase and counterclockwise to decrease, reading the voltage in the
BSLSTMs digital display.
Stimulator Safety Features
The stimulator cannot operate unless its Output Control panel is open.
The Pulse ON/OFF Switch on the Stimulator Output Control panel must be OFF in order to open and configure
Stimulator Preferences.
If the Stimulator Output Control panel (or the AcqKnowledge application) is closed in the middle of a pulse
train while the stimulator is running, the stimulator will shut down and the pulses will stop.
If another data acquisition window is activated, the stimulator will stop and remain OFF unless restarted using
the parameters associated with the new data window. The only exception is that if the stimulator is ON and the
data window corresponding to current stimulator parameters is acquiring data, then the stimulator will continue
to run until the end of the acquisition.
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Chapter 11 Set Up Event Hotkeys
Events (Markers)



Event Toolbar Event Insertion Event Control
Event (Marker) Overview
For detailed analysis, it can be useful for waveforms to have extra information associated with them. This
information might include waveform boundaries from ECG analyzers, spike classifications from a spike sorter,
heartbeat classification from a PhysioBank file, or even detailed user notes. AcqKnowledge 4 uses event
functionality to store and manage this information.
An event is a piece of information associated with a specific time in a waveform. An event can capture points of
interest within a file (i.e. subject moved, dose added) or on a particular channel (i.e. T-wave onset). Once events
are marked in the file, AcqKnowledge can use the event information for analysis, including measurement (page
217) and cycle detection (page 307).
An event has the following pieces of information associated with it:
o Event type
o Sample location: the time position in hardware samples where the event is defined.
o Channel: the channel for which the event is relevant.
o Some events, such as the time of the start of an appended segment, may be relevant to all of the
channels of a graphthese are Global events.
o Label: a string of text that can be entered either automatically or by the user to provide more
information about an event. Labels can be fixed or sequential in AcqKnowledge 4.2 and up.
Different event types can be entered automatically or manually. These different event types allow
events to be filtered and also support analysis routines that key off of these events.
o Event insertion tool
o Set Up Manual Event Hotkeys (see page 205) to manually insert events during acquisitions
o Copy/paste measurements and Copy/paste wave data operations can insert events at the
selection boundaries; choose Mark with events under Preferences (see page 204)
o Cycle Detector Output Events option (see page 307)
o Contextual menu in Event region

o Specialized Analysis (see page 331) to automatically insert events according to complex
analysis algorithms

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Part C Analysis Functions 203
Event Toolbar

The event toolbar displays global events and provides a quick editing area for event descriptions. The right
button toggles visibility of the Event Palette for detailed control (see page 206). The palette will refresh when
events change the event configuration, such as horizontal scrolling, scale changes, changes in the selected event
via clicking in the graph window, editing of the event label by using the event bar, transformations that define
new events for the graph, waveform editing operations, and additions of new events by clicking the event bar at
the top of the graph window.

Event Tooltips
If events are being displayed within the plotting area and tooltips are enabled, a tooltip will be associated with
every event in the plotting area. The tooltip includes the event type description, the user-defined label (if
present), the time location of the event, and the amplitude of the waveform at the event location. While this
information can be drawn directly on the graph, event tooltips assist in browsing event information when the
screen becomes too crowded and there is not enough room to display all of the times, amplitudes, and labels.
Event tooltips are displayed under the event icon.
If the event is being plotted directly on the waveform, this will be the point on the waveform associated
with the event.
If there is an indicator and the event icon is at the top of the indicator, the tooltip will be anchored at the
top of the indicator.
If the events are being plotted at the top of each track, the tooltip is anchored at the top of the plotting
area directly underneath the event icon.
Event tooltips will not be displayed if tooltips are disabled, if events are only being displayed in the events bar
at the top of the screen, if X/Y mode is in use, or if events are not currently visible.
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Event Preferences

Preferences > Event Summary and Waveform
Use the Event Summary section of the Preferences dialog to set options for pasting summaries of events into
the journal. (Preferences shown above and listed below are from AcqKnowledge 4.2)
Group events
Sorted by type sorted by event type descriptions first
Sorted by channel grouped based upon where they are defined (Global events appear first, followed
by groups for each individual channel).
Sort Grouped events
Sorted by time sorted in order by increasing time
Sorted by label sorted alphabetically by label
Include only events visible on the screen
Determine if the summary is generated for all of the events that are in a graph, or only for those events
that are currently visible on the screen. If there are thousands of events in a file, this feature allows the
list to be pared down to those of interest.
Event summary options will be saved with the graph if the graph has a graph journal, and can be pasted into the
journal using Summary in Journal Event Palette Actions command (see page 210).
Other event preferences are available under Preferences > Waveforms
- Mark waveform edits with events
- Mark selection with events in graphcreate events at data selection bounds. This includes selection
events (selection begin and selection end) for global events when measurements or waveform data are
pasted. When selected, measurement pasting will result in an automatic execution of the Mark
Selection feature manually accessible from the Event Palette.
- Include time value include the time value (relative to start = 0) for the paste.
- Include timestampInclude time and date stamps for when the paste occurred; this timestamp will
match any timestamp pasted into the journal. When selected, any selection events added to the graph
will have their labels set to match the timestamp.
- Auto-paste results in independent journal (Preferences > Journal)Selection events and time
stamp events can be automatically inserted to an independent Journal.
Combine these options to retain enough information to reproduce measurement results and correlate
measurement results with specific areas of the graph; this helps verify the accuracy of measurement results
made through manually constructed graph selections.
Any change to these settings will be retained within a saved graph file and will become the default for newly
constructed graphs.
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Part C Analysis Functions 205
Event Hotkey Setup

Events of different types
can be inserted during
acquisition, whether or
not events are visible in
the graph. When a hotkey
is pressed during
acquisition, an event will
be inserted into the graph
at the end of the most
recently acquired data.
Each hotkey can have a
different configuration,
adjustable through a
dialog accessible via the
MP > Set Up Manual
Event Insertion
Hotkeys... menu item.
Hotkey Assign Escape or F1 through F9. When a different hotkey is chosen, the other controls of the
dialog change to reflect the configuration of the new hotkey.
Action Choose whether the Hotkey assignment creates an event or a focus area.
Event type Lists the standard hierarchical menu of available event types; Types are detailed on page 211.
Choosing a new type from the pull-down menu will change the type of event inserted when the
hotkey is pressed during acquisitions.
Channel Contains a Global entry and all of the channels (analog, digital, or calculation) set to
Acquire in Set Up Channels.
Global will define global events drawn in the event bar above the graph data
Choosing a new channel from this menu will cause events to be inserted on the appropriate
channel of the graph when the hotkey is pressed.
Label Edit field for label text and toggle optional inclusion of time stamp and/or date stamp. Stamps
correspond to the time of the system clock when the key was pressed, that is, the time of the
event insertion in real clock time.
Fixed - Provides a fixed label from text entered into the label field to the right. This label is
used every time the assigned hotkey is pressed. (AcqKnowledge 4.2 and higher)
Sequential - Labels for events will iterate sequentially through the entries in the table index
when the assigned hotkey(s) is pressed. The area under Label is editable for entering text.
(AcqKnowledge 4.2 and higher)
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Additional Hotkey Setup Controls Function
Add Adds an editable label field to the list.
Rename Allows renaming of the existing segment label.
Delete Deletes a selected custom label.
Delete All Deletes all custom labels.
Up Incrementally moves a selected label up the list.
Down Incrementally moves a label down the list.
Top Moves a selected label to the top of the list.
Bottom Moves a selected label to the bottom of the list.
Include time Adds timestamp to labels when checked
Include date Adds current date to labels when checked
Create/Toggle Focus Area Action
Selecting the Create/Toggle Focus Area action presents a similar setup dialog, but dictates that hotkeys setups
will be assigned to defining Focus Areas instead of inserting events.

When this option is chosen, pressing an associated hotkey during a recording will initiate a focus area in the
graph. Toggling the same hotkey will conclude the focus area. The focus area will appear highlighted and
outlined in the graph following the second (termination) keystroke. As with events, multiple hotkeys and labels
can be assigned.
Example for setting up a Focus Area Hotkey:
1. Choose the desired hotkey from the Hotkey list.
2. Under Action, select Create/toggle focus area.
3. Assign the focus area a label by typing it into the Base focus area label field.
4. If additional focus area hotkey assignments are desired, choose another hotkey
from the list, and repeat steps 2 and 3.
5. When focus area hotkey assignments are completed, click OK.
If the same hotkey combination is repeated to create subsequent focus areas, the base focus area
label will remain the same but with incrementing numbers appended to the title.
If a different hotkey combination is used for subsequent focus areas, unique base focus area names
will be used as assigned.
Starting a focus area assigned to one hotkey and then starting another focus area assigned to a
different hotkey will terminate the original focus area and start a new one.
Focus areas can be created and toggled while a recording is in progress.


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Part C Analysis Functions 207
Event Palette



The event palette is a floating window that
provides a quick summary of events for the
top most graph and can used to examine,
search, and modify events. Events can be
extracted in a time range for a specific
event type and specific channels.
There is only one visible event palette for
the entire application. The palette consists
of four sections: event list, selected event,
display, and event actions. Each section
can be shown or hidden by toggling the
disclosure button next to its title.
C Event List, see page 207.
C Selected event, see page 208.
C Display, see page 208.
C Actions, see page 210.
o See the Event Journal
Summary enhancements.
Event List

The event list provides an expandable, scrollable,
hierarchical view of the events in the topmost graph.
Events are grouped by their channel on the top level.
The event list has three columns of information:
Events: the readable type for each event
Location (Time): the time location for each event
Label: the user defined description for the event.
Sort the contents in ascending or descending order on each column by clicking the column header. Events and
Description will sort in standard alphabetical order, Location will sort based on the numerical sample location
of each event.
Select a single event from the event list by clicking on a single event. The event will be selected in the graph
window and made visible if it is not currently displayed.
List visible events only toggles the checkbox to switch between the two display modes.
When enabled, the event list will display only those events that are being displayed on the plotted portions
of the graph. As the user navigates through the graph with the scrollbars, horizontal scale, or other means of
changing the amount of visible data, the event list will continually refresh to contain the new set of visible
events.
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When disabled, the event list will display all of the events for the entire graph. This can allow for easier
navigation through graphs with hundreds of events, such as PhysioBank files.

Selected Event



Event type options are
detailed on page 211.
When a single event is selected, the type, channel (or General for global events), user-defined label, and
location of the event will be filled in and can be edited. The controls can display information about only one
event at a time; if no event is selected, the controls will be grayed out.
Event Location
Location defines the position where the selected event occurs, relative to the first sample in the file. To change
the location of an event, change the position entered in the Location box. Precision matches the horizontal axis
setting.
Events may also be repositioned using the mouse. Option-click the event icon in the graph and hold down the
mouse while dragging; the event will be repositioned at the horizontal position where the mouse button is
released.
Display

Event display location Event display detail
Display controls determine the location and detail of events to be drawn in the frontmost graph.
C LocationChoose one of the five display methods (described on page 209).
C Detailthe three checkboxes to establish how much information to include with events.
C Indicator lengthSet the slider to shorten or lengthen the indicator line. This option is only active if
the display mode is On waveform, with indicator or At top, with indicator.
C Font Align Selects font style and alignment of Event labels.
C Angle Determines the angle in degrees that the Event text can be displayed in the graph. Value can
be positive or negative.
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Part C Analysis Functions 209

Location & Display Description
In event bar

Event icons are displayed in the global events bar located on top of the plot area in the
graph window. This does not allow for distinguishing what channel a specific event
belongs to.
To select the event, click the icon in the events bar.
On waveform

Event icons are displayed above or below the actual sample in the source channel
corresponding to the location of the event.
To select the event, click the event icon on top of the waveform.
Top of plot

Event icons are displayed at the top of the channel track, either on top of the grid or in
a channel-specific events bar.
To select the event, click the icon at the top of the channel track.
On waveform, with
indicators

Event icons are displayed above the data with a vertical line of configurable length
running through the data sample of the source channel at the events location.
To select the event, click the event icon or the indicator line.
Top of plot, with
indicators


Event icons are displayed at the top of the channel track with a vertical line of
configurable length running through the data sample of the source channel at the
events location.
To select the event, click the event icon or the indicator line.
Detail When an event is being plotted within a graph, either on the top of a channel or
floating above the data, the event's location, description, and amplitude of the
waveform at that location can optionally be displayed along with the event icon.
Plotting of additional information can be used for graphical annotations on the data
and for clarifying event location for hardcopy or presentation.
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Actions

Actions Button Description
Find It is easy to create many more events then one can easily scroll through and locate
in a list. Find controls the automatic location of events based on established search
criteria.
Click the Find button to generate the Event search criteria dialog, and then
combine or restrict information to define desired events: event type, specific
channel location, or label search.
Click Find First to search for the first event in the graph that matches the
criteria. If found, the event will be selected and made visible in the graph window.
Find Next Finds the next single event that matches the established search criteria until no
remaining events match the search criteria.
Cut Selected Event Active only when an event is selected, removes the selected event from the graph.
Clear
Clear all
Generates a search criteria dialog (identical to the Find dialog) and removes all
matching events from the graph.
Summarize in
Journal
Displays a dialog with controls that affect which events are included in the
summary.
Events can be filtered by visibility on the screen. Creates a textual summary of all
of the events in the journal.
See Event Preferences on page 204 for more information about
modifications to the traditional events summary.
Event Journal Summary Enhancements

Events to be included in the summary can be filtered using the same criteria as
Find... in the Event Palette. By adding the ability to summarize only events
matching specific criteria, textual reports of arrhythmias or other infrequently
occurring events of interest can be generated with ease.
When Summarize in Journal is clicked on the event palette, a dialog will be
displayed with controls that affect which events are included in the summary.
If there is no journal for the current graph, you will be prompted to create a
journal.
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Part C Analysis Functions 211

Mark Selection Defines two new Global events in the graph at the precise time locations of the
currently selected area (the highlighted wave data section). If there is no selection
in the graph, this button has no effect. The events that are inserted will have the
Selection Begin and Selection End event types.
Restore from
Snapshot
Enables deleted events to
be restored from events
present in a Data Snapshot.
This option becomes active
only if a Data Snapshot of
the main graph is
displayed. The following
prompt will be displayed
when Restore from
Snapshot is selected.
Event Type Options
Event Types are pre-defined options for assigning event information. The Event Type is for marking purposes
only and does not imply any analysis has or will occur for the event (unless Specialized Analysis was
performed, see page 331).
Once Event Types are defined, some analysis functions can be automated, including measurement (page 217)
and cycle detection (page 307).
Event classifications:

Event classifications group similar event types together into a logical category.
Event classifications present event types in a hierarchical fashion and allow other
event classifications to be contained within them.
For example, the Hemodynamic event classification includes a Beats sub-class
with pre-ventricular contraction and escape beat event types.
Event type Classification
Global This is the same as untyped markers from AcqKnowledge 3.6 or earlier. Unrecognized event types
will be classified as global events.
Append Automatically inserted by the program on append operations. Custom Append labels can be
created in MP > Set Up Segment Labels. (See page 223.)
Notes Annotation event to add notes on the data.
User-defined Hotkey insertion for user-specific events; 9 types can be inserted via the keyboard during
acquisition.
Pharmacology Basic pharmacological events: baseline, washing, and dosing.
Waveform Edits Automatically inserted by the program on cut or paste operations in a graph file. The description
consists of the edit operation performed and a timestamp.
Insertion of waveform edit events is off by default, but can be turned on for GLP purposes.
Selections Used to mark boundaries of selected areas.
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Classification Pre-defined Event Type Options
Default Esc key inserts global event.
General Waveform onset or end Maximum and minimum
Change in signal quality or rhythm Reset
Recovery Append
Hemodynamic
> Beats
Normal Nodal premature
Paced Supraventricular premature
Fusion of paced and normal Premature ventricular contraction
Unclassifiable R-on-T premature ventricular contraction
Left bundle branch block Fusion of ventricular and normal
Right bundle branch block Atrial escape
Bundle branch block Nodal escape
Atrial premature Supraventricular escape
Aberrated atrial premature Ventricular escape
Hemodynamic
> Blood Pressure
Systole End Systolic pressure
Diastole End Diastolic pressure
Hemodynamic
> ECG Complexes

QRS onset, peak, and end U-wave peak
T-wave onset, peak, and end PQ junction
P-wave onset, peak, and end J-point
Q-wave peak ST segment change
S-wave peak T-wave change
Hemodynamic
> Impedance
A-point O-point
B-point X-point
C-point Y-point
Hemodynamic
> Monophasic AP
Plateau Upstroke
Hemodynamic
> Other
Start of ventricular flutter Pacemaker artifact
Ventricular flutter wave Isolated QRS-like artifact
End of ventricular flutter Non-conducted P wave
Notes Arrowshort, medium, or long Star
Flag
Pharmacology Baseline Wash
Dose
Neurophysiology Spike Episode Begin Spike Episode End
Respiration Inspire Start Inspire End
Apnea Start
Stim/Response Stimulus Delivery Response
EDA Skin Conductance Response Specific SCR
Clustering Cluster 1-9 Cluster n
End Cluster Outlier
Training Set
User-defined User Type 1-9
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Part C Analysis Functions 213

Classification Pre-defined Event Type Options
Waveform Edits Cut Paste end
Paste begin
Selections Selection begin Selection end
B-Alert Start of Eye Blink Artifact End of Eye Blink Artifact
Start of Excursion Artifact End of Excursion Artifact
Start of Saturation Artifact End of Saturation Artifact
Start of Spike Artifact End of Spike Artifact
Start of EMG Artifact End of EMG Artifact
Workload EMG Start Workload EMG End
Workload Invalid PSD Start Workload Invalid PSD End
Dummy Data Start Dummy Data End
Misaligned Data
BioHarness Button Pressed
SMI Import Left eye hit object Right eye hit object
SMI stimulus image has been presented to the subject
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Event Measurements
Measurements are a quick way to extract information from a graph. Three measurements extract information
from events. When combined with the Cycle/Peak Detector (page 307), they are also powerful data reduction
tools. These event measurements can provide quick summaries of event information, compute mean intervals
between event types, and detail other operations.
evt_ampl Event Amplitude Measurement (see below)
evt_count Event Count Measurement (see page 215)
evt_loc Event Location Measurement (see page 215)

Event Amplitude Measurement

evt_amp Extracts measurement results where events
are defined. Note that the amplitude is always taken from
the measurement channel, which may be different from the
channel on which the events are defined. Useful for
extracting information such as the average T wave height
within the selected interval. The measurement result is
displayed without units (matching Value and other
amplitude events).
Select Event Amplitude or click the measurement info
button to generate the settings dialog.
Event Type Determines the type of events that will be processed; Types are detailed on page 211.
Location Determines where the processed events need to be defined. The menu options are:
Measurement channel onlyOnly extracts amplitude values for events that are defined on the
channel specified in the measurement channel pull-down menu. Global events and other
channel events are not included.
Global events onlyOnly extracts amplitude values for events that are defined as global
events appearing in the events bar; changing the measurement channel will not affect the
measurement result. Channel events are not included.
AnywhereExtracts amplitude values for events defined on any channel and also global
events; changing the measurement channel will not affect the result
Extract Determines what processing will be performed on the amplitude values extracted from events that
match the Type and Location settings. The processing options are:
Amplitude at first event onlyThe value of the measurement channel at the time of the first
matching event in the selected area.
Amplitude at last event onlyThe value of the measurement channel at the time of the final
matching event in the selected area.
Sum of amplitudes at all eventsComputes the sum of the value of the measurement channel
from each matching event within the selected area.
Mean amplitude from all eventsComputes the average amplitude value of the measurement
channel from all of the event locations within the selected area.
Minimum amplitude from all events
Maximum amplitude from all events
If there are no matching events of the selected type in the selection, the measurement result will be zero.
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Part C Analysis Functions 215
Event Count Measurement

evt_count Evaluates the number of events within the
selected area. The measurement result is unitless.
Select Event Count or click the measurement info button to
generate the settings dialog.
Event Type Determines the type of events that will be counted; Types are detailed on page 211.
Location Determines where the counted events need to be defined: the pull-down menu options are:
Measurement channel onlyOnly includes events that are defined on the channel specified
in the measurement channel pull-down menu; global events and other channel events are not
included.
Global events onlyOnly includes events that are defined as global events appearing in the
events bar; channel events are not included. Changing the measurement channel will not
affect the measurement result.
AnywhereIncludes events defined on any channel and also global events. Changing the
measurement channel will not affect the measurement result.
If there are no matching events of the selected type in the selection, the measurement result will be zero.

Event Location Measurement

evt_loc Extracts information about the times of events.
The measurement result will take on the units of the
horizontal axis; if specific units were set for time or
frequency via Preferences, those units will be used.
Select Event Location or click the measurement info button
to generate the settings dialog.
Event Type Determines the type of events that will be processed; Types are detailed on page 211.
Location Determines where the processed events need to be defined. The menu options are:
Measurement channel onlyOnly extracts the time of events that are defined on the channel
specified in the measurement channel pull-down menu; global events and other channel
events are not included.
Global events onlyOnly extracts the time of events that are defined as global events
appearing in the events bar; channel events are not included. Changing the measurement
channel will not affect the measurement result.
AnywhereExtracts the time of events defined on any channel and also global events.
Changing the measurement channel will not affect the measurement result
Extract Determines what will be extracted from events that match the Type and Location settings:
First event location onlyThe measurement will equal the time at which the first matching
event in the selected area is defined.
Last event location onlyThe measurement will equal the time at which the final event
within the selected area is defined.
Sum of all event locationsThe times at which all matching events are defined are added
together to produce the measurement result. This sum of times can be combined with Event
Count measurements to compute average intervals over the selected area.
If there are no matching events of the selected type in the selection, the measurement result will be zero.

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Printing Events
When a graph is printed and events are displayed onscreen for the graph, event icons will print as they are
displayed. Event icons will be scaled, depending on the printer's DPI, to be proportional to the vertical scale
plotted on the screen. If events are located at linearly interpolated positions, event icons will be dimmed on the
printout (see the Variable Sample Rate section).
Event display setting Printed result
Global events Global events are drawn above and outside of the data plotting rectangle in the
printout. If the event labels are close together, their alignment will be staggered to
show separate lines of label text. (AcqKnowledge 4.2 and higher)
In event bar All events are drawn above the data area of the printout. Only labels may be drawn
with the events.
Top of plot or
Top of plot, with
indicator
Channel-specific events are drawn at the top edge of their channels track. No
indicator lines are drawn. Depending on the display settings of the graph, the event
label, amplitude of waveform at the event location, and Time of the event may be
printed below the event icon
On waveform or
On waveform, with
indicator
Channel-specific events are drawn immediately above the position of the
waveform sample at their location and will appear to be printed immediately above
the data of the waveform. No indicator lines are drawn. The vertical printing
position of an event icon will be identical for On waveform and On waveform,
with indicator displays. Depending on the display settings of the graph, the event
label, amplitude of the waveform at the event location, and time of the event may
be printed above the event icon.
Draw vertical divider at event locations option in the Print Setup dialog.
Enabled: draws a dashed vertical line at the precise time location of each event. Vertical divider lines for
the event type will extend
Global Through all channels of data
In event bar Through all channels of data
Top of plot From the top to the bottom of the relevant channel track
On waveform From the top to the bottom of the relevant channel track
Disabled: prints only the event icon, label, amplitude, and time. No indicator lines will be printed for the
event display. The vertical divider can be used in place of indicator line drawing.

Event Selection
Individual events can be selected according to click locations.
When an event is selected, the event icon will be drawn based on the graphic type:
Specific selected graphicthe selected graphic is drawn or if none, an inverted global graphic.
No associated graphicsthe global event graphic will be used.

Events and Graph Selections
When an event on a waveform plot occurs within a selected area of the graph, the event icon and indicator line
(if present) will be inverted along with the grid, background, and wave data. Event types that don't have a
selected graphic will appear as global events if the events are selected events and they are contained in an I-
beam selection.
Visit the online support center at www.biopac.com
Part C Analysis Functions 217
Events and Waveform Editing
Waveform editing will adjust event locations for channel-specific events. Waveform editing will never alter the
time values for Global events (not associated with any specific channel, such as append events).
Copy When a portion of a waveform is copied the channel events will also be copied to the clipboard.
Cut When a portion of a waveform is cut, any channel events within that selected area will be removed and
channel events to the right of the removed area will be shifted to the left.
If waveform editing event insertion is active, a waveform edit event will be inserted at the location
of the edit operation indicating a Cut operation in its description.
Paste When the waveform is pasted from the clipboard, the channel events will appear at their same locations
and any channel events to the right of the end of the pasted segment will be shifted by the length of the
pasted segment.
If waveform event insertion is active, a waveform event marker will be inserted at the beginning
and at the end of the pasted segment.
Constructing Graph Selections from Events
Graph selections can be defined from events (in addition to the I-beam tool). Holding down the
Command/Open-Apple key while double-clicking an event icon in the graph window will place a cursor at the
event location; this is a zero-width selection, equivalent to single-clicking with the I-beam tool without
dragging.
To create a graph selection from events, hold down the Command key and select an event by clicking on
the event icon in the graph window or its entry in the event list.
To align the boundaries of the graph selection with the time of the previously selected event location and
the time of the newly selected event, hold the Command key when selecting the new event.
To make a graph selection match the time between two events, click to select the first event, hold down the
Command key, click again to select the second event. On this second click, the selected area of the graph
will change to align with the two events.
Event Plotting and Variable Sampling Rate
Event positions are defined in terms of the hardware sampling rate. The Variable Sampling Rate feature can
generate waveforms with a sampling rate lower than the hardware sampling rate. Through explicit event
definition, waveform downsampling, or other operations, events on a downsampled channel may not align with
an actual waveform sample, but rather occur at a hardware sample position in between waveform samples.
These events will be drawn using linear interpolation when applicable, and only if the waveform is being drawn
in line plot mode. In step plot and dot plot modes, regular event drawing routines will be used with the vertical
position and amplitude of the nearest waveform sample to the events left.
When an event is to be drawn on an intermediate position on a waveform, the linearly interpolated value will be
calculated for the hardware sample location. The interpolated value will be derived from the closest waveform
sample to the left and to the right. The vertical position on the waveform of the event and indicator line will
match the vertical position of the linearly interpolated sample amplitude. This will place it immediately above
the line connecting the two waveform samples on screen.
If an event is being drawn using linear interpolation
Event icons will be dimmed, regardless of their display position (on waveform or top of the plot).
Indicator lines will be drawn on the waveform at a linearly interpolated position and the indicator line will
be a gray dashed line instead of a solid black line. (Indicator lines are never printed.)
Amplitude labels, if included with the event, will correspond to the linearly interpolated amplitude at the
event location and the linearly interpolated amplitude will be drawn in italicized text.
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Chapter 12 Other MP menu Commands

BioHarness users should see the BioHarness User Guide available under
the Help menu and installed to the User Support folder in the program folder.
Show Input Values

The Show Input Values option of the MP menu generates an Input Values window, which displays channel
values in real time, whether an acquisition is in progress or notwhich allows you to display values prior to or
after an acquisition.
The Input Values display can be set to numeric, horizontal or vertical bar graph format, and it can be resized
and moved to any position on the screen. To set the display mode, use the Mode menu generated via the
Options button.
Note The Input Values window only displays values for channels that were Set Up with the Values box
checked (see page 107 for more information).
Hold Regardless of the display options selected, the display can be frozen at any point in time by
clicking the Hold button. Clicking this icon will hold the values at their level(s) when the icon
was pressed. The window will remain frozen until the icon is clicked again. Once the values
are unfrozen, the values will return to the standard real time display mode.
Options


Mode controls the format of the values display.
- Numeric Valuesdisplays the voltages of the appropriate channels numerically.
- Bars: Horizontal bars or Vertical barsthe range of values of the bar graphs
corresponds to the range for that channel in the graph window. To see the bar bounce
less for a particular channel, increase the units per division; to fill more of the window
space, decrease the units per division in the graph window.
Font and Size determine text display from fonts installed on your computer
Precision controls the total number of digits displayed.
Show controls the amount and type of information displayed regarding each channel. Click in
the box next to each option to activate it.
- Channel Numbers will display the channel numbers (A1 for the first analog
channel, for example).
- Units will display the units for each channel (as indicated in the main graph
window). By default, each channels display units are scaled in terms of Volts,
but this can be changed by clicking in the amplitude scale units area in the graph
window.
- Labels will display the channel labels (ECG 1, Respiration, etc.) along with the
input values. This feature is especially useful when values from multiple
channels are being displayed simultaneously.
- Min/Max will display the range of values associated with the data. This range
corresponds to the upper and lower display limits for each channel as it appears
in the graph window.
- Values will display number values along with the horizontal or vertical bar chart.
Visit the online support center at www.biopac.com
Part C Analysis Functions 219
Manual Control

STM100 option
The Manual Control dialog allows you to monitor and/or output pulses through the digital input/output (I/O)
channels, as well as manually set the magnitude of the signal on either of the analog output channels. The
digital outputs in Manual Control cannot be used to trigger an online Averaging acquisition.
Stimulator Usage Note
Use Manual Control to specify the stimulation output level
a. If the wide range of waveform output options available in the Stimulator Setup dialog cannot
match your specifications.
b. For pre-stimulation and post-stimulation.
See page 172 for important Analog Output details
The 16 digital channels are sectioned off into two blocks, with the first block consisting of I/O channels 0
through 7, and the second block consists of I/O 8 through 15.
- All the channels within a given block are programmed together and can be set as either inputs or
outputs.
- The two blocks can be set independently.
o In other words, the lower block can be set to input data while the upper block outputs data. You
can set channels in the lower block to either read in data or do nothing (as opposed to
outputting data) while channels in the upper block either output data or do nothing (as opposed
to reading data).
To read incoming values for a given block of digital channels, click the Input button below the row of channels
for which you wish to have input values displayed. This enables a block of digital channels to receive incoming
data. To read the values for the entire block simultaneously, click the Read button to the left of the channel
boxes for that block. Since these are digital channels, the values on the individual channel boxes will toggle
between 0 and 1.
- When AcqKnowledge is launched, values for digital channels #0-7 always read "0" and #8-15 always
read "1" to allow for compatibility with the STM100C module, which utilizes the lower eight digital
lines for attenuation control.
When Read Continuously is enabled (below the Input button), the values will be read in real time. When
unchecked, the displayed values correspond to the values for that block of channels as of the last time the Read
button was depressed. This mode provides much the same information as the Show Input Values mode.
To output values for a given channel, the block containing that channel must first be enabled to output data. To
do this, click the bar below the channel boxes so the button reads Output. You can then program the
individual channels within that block. These channels will toggle between 0 and 1, with a 0 corresponding to
zero Volts and a 1 corresponding to + 5 Volts. To output a digital 1 on I/O channel 3, the dialog would be setup
as shown above.
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220 AcqKnowledge 4 Software Guide
The function buttons toggle as follows:
Input toggles to Output When Input is selected, the checkbox is Read continuously.
Set toggles to Read When Output is selected, the checkbox is Set immediately.
To output a signal on Channel 3, click the Set button to the left of the channel box. If the Set immediately box is
checked, the signal will be output when the channel button is clicked.
IMPORTANT
Potential use conflicts can arise between the parameters set in the Manual Control window and
those set for digital channels in the Set Up Channels window.

STM100 option

STM100 option
When the STM100C stimulator module is connected to an MP150 System, the output level can be controlled
via the STM100 option of the Manual Control dialog.
Attenuation Attenuate the output signal by a given number of decibels (dB) for controlled stimulus
applications. To output a signal with no attenuation, simply set the Stim 100 Attenuation to 0
dB.
Manually outputting a value on a digital channel can stop an acquisition if data is being
collected at very high speeds (greater than 10,000 samples per second aggregate).
Invert output Check this box to invert the polarity of the signal output through the STM100C.
This function can also be achieved by flipping the polarity switch on the STM100C from
positive (POS) to negative (NEG).

For more information on the STM100C stimulator output module, see the BIOPAC MP Hardware Guide.pdf.
Set Up Linked Acquisitions
This MP menu option allows acquisitions to be configured and recorded simultaneously from different
hardware devices types over separate graphs. In order for Linked Acquisitions to function, each selected graph
must be connected to a different MP unit or playback data source. (If two or more graphs are connected to the
same MP unit, the linked acquisition session will not start.)
To add or change the MP device to any open graph, click the Connect to: toolbar button and select or add a
new device from the menu.

The linked acquisition can output recorded data into the separate graphs, or optionally, merge the data into one
graph. If the latter option is chosen, data from the separate graphs will be contained in separate labeled channels
within the merged graph.
Visit the online support center at www.biopac.com
Part C Analysis Functions 221
The sample rates and recording duration can vary between the linked acquisition graphs, but all recordings are
limited to Save Once to Memory mode. Append or Disk modes are not supported in linked acquisitions.

Top Column Description
Graph Title Displays the titles of the linked graphs.
Acquire Includes or excludes graphs from linked acquisition.
Status of
Hardware Device
Shows current status of hardware.
Master Synch.
Dev.
Indicates the MP hardware providing the synchronization signal. This option is supported in
MP150 hardware only.
Name of
Hardware Device
Identifies hardware device linked to graph.

Functions Description
Merge results into new graph at the end of
acquisition
Outputs data collected from multiple recordings into one graph.
Resample merged data to: highest acquisition
sample rate
Data in all graphs will be resampled to highest used sample rate
among all graphs in the set.
Resample merged data to: lowest acquisition
sample rate
Data in all graphs will be resampled to lowest used sample rate
among all graphs in the set.
Specify synchronizing method Offers various options for synchronizing the linked acquisitions.
Use the timestamp method Compares all timestamps, detects the one with the latest time, and then cuts the
beginning section of the data in each channel. Playback mode is not supported in this mode
Use the master synchronization method Used specifically for pairing and synchronizing data obtained during
linked MP150 and B-Alert acquisitions. This is the only option where the Master Sync Device radio button is active.
Use simple cutting of data method Searches for the shortest acquisition length and uses this parameter to
calculate how much data will be removed from the beginning of longer acquisitions. This is the least precise of the
three synchronization methods.
Start Acquisition Starts the recording for all selected graphs.

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Limitations on Linked Acquisitions synchronization methods
Synchronization Mode Description Criteria
Minimum number of selected
graphs
2
Minimum number of analog
channels
1
Any method
Minimum length of acquisition
when B-Alert device is used
12 sec.
Allowed hardware types MP150 and B-Alert only Master synchronization device
method
Minimum sample rate on first
channel of B-Alert hardware
256 s/s
Linked acquisitions and wireless connections: In general, if the computer is trying to use multiple network
cards at the same time with an MP150, the MP150 either needs to be on the primary network, or additional
network cards must be disabled, or network bridging must be enabled in the Windows system settings. When
self assigning IP addresses, the MP150 may also choose a new IP address each time it is power cycled, which
will prompt for reconnection.
Manage Hardware Connections




The Manage Hardware Connections option
enables easy connection and disconnection
of new hardware, and allows switching
from a particular hardware unit (or
hardware type) to another. The following
controls are available:
Connect New Hardware
Choosing Connect New Hardware opens a
dialog for selecting and adding additional
hardware units. Once a new hardware unit
added, it will be available for use in the
application, and will appear in the
connected hardware list. (The example at
left shows the selection of additional
MP150 units on a local area network.)
The Choose MP150 pull-down menu lists
all MP150 units that are powered ON and
sitting on the same local area network. The
software cant determine the lock status
until a user attempts to communicate
directly to a MP150 uniteach MP150 unit
needs to be tried to determine if it is locked
or unlocked.
Disconnect
Use to disconnect from any available
hardware in the list.
Playback from Graph
Use as a shortcut to enter Playback Mode.
For more information on Playback Mode,
see page 42.
Visit the online support center at www.biopac.com
Part C Analysis Functions 223
The fact that MAC (Ethernet) addresses appear in the users Select MP150 dialog does not imply that the
MP150 unit is, in fact, unlocked and available. If a user attempts to connect to a locked MP150, an error
message will be generated to advise that the MP150 unit is locked to a different computer.
AcqKnowledge locks an MP150 as soon as it connects to it, which tells the MP150 to only respond to
commands from that particular computer and the communication method (serial or Ethernet). The lock has a
timeout which is reset every time the MP150 unit receives a command from the computer that locked it. To
locate MP150s in the local network, AcqKnowledge sends a broadcast packet to the local area network that asks
all the MP150s in the network to respond. All the MP150swhether locked or unlockedwill respond to this
prompt. This means that the Select MP150 menu may allow a user to select an MP150 that is locked. In such
cases, AcqKnowledge will fail to connect (to a locked MP150 unit, as expected). To resolve this issue, unlock or
power cycle the MP150 unit. See Locking/Unlocking the MP150 (Appendix Epage 488) for more details.

MP150 Info
Select MP150 Info from the MP150 menu to generate a dialog with information about the software and
firmware versions being used by AcqKnowledge:

Manufacturer ROM is the factory-installed firmware version; check this before you Reset the MP150 unit for
a Firmware Rollback (see page 490).
Factory-installed Firmware version 1.1.2 or previous (purchased approximately November 2002 or
before) may not reset to a level compatible with UDP communication. In such cases, you will need to
install AcqKnowledge 3.7.2 or previous (non-UDP) and update to UDP in stages; contact BIOPAC for
additional support.
Note: For information about AcqKnowledge software, click Help > About AcqKnowledge.

Update Firmware
This menu item is used to upload MPB firmware files provided to you by a BIOPAC support technician. Unless
a firmware warning is displayed at application launch, your MP150 already has the latest firmware revision and
no further action is necessary. If a firmware warning is displayed, contact BIOPAC technical support for more
information.

Segment Labels
Selecting Set Up Segment Labels from the MP menu launches a setup dialog enabling assignment of user-
defined labels to append event segments. The Segment Label options are applied to the active graph only. The
selected settings will be saved with the graph, but will not be applied globally to existing or subsequent graphs.
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224 AcqKnowledge 4 Software Guide


Add Adds a segment number to index. Segment text can be edited under Label.
Rename Used to rename an existing segment label.
Delete Deletes a selected segment from Index.
Delete All Deletes all segments from Index.
Up/Down Incrementally moves a selected segment up or down the Index.
Top/Bottom Moves selected segment to top or bottom of Index.
Enabling checkboxes below the icons adds time/date stamps to the segment label.

NOTE: Set Up Segment Labels option is available in AcqKnowledge 4.2 and higher only.
Sound Feedback
Set Up Sound Feedback generates a setup enabling acquired data to be redirected to the computers default
audio output device. This feature can be used to monitor waveform data as sound through the computer
speakers or headphones. (AcqKnowledge 4.2 and higher only)

SOUND FEEDBACK
CONTROLS
FUNCTIONS
Sound enabled Turns sound feedback of data on and off.
Output Sampling Rate Selects from available sampling rates of the default audio device.
Source Channel Selects the analog, digital or calculation channel from which the audio will be acquired.
Reset Adaptive Gain Control Resets gain control to adapt to the current level of the signal. Use after sound feedback
has started to re-adjust the level after accidental spikes or large artifacts.
Enable low pass filter Applies a low pass filter at the Nyquist frequency (50% of the acquisition sampling rate).
This IIR filter can help smooth out transition artifacts due to upsampling of data to the audio
sampling rate. (Enabled by default)
Median removal controls
(Window width, Recomputate)
Removes baseline offset from the output signal.
Window width Sets width of median removal window (in seconds). Must be a positive value.
Recomputate every Provides the time duration (in seconds) after which the median of the data is regenerated
from the raw source data. Must be a positive value.
Visit the online support center at www.biopac.com
Part C Analysis Functions 225
Gauge

The Gauge is accessed
via MP150/MP36 >
Show Gauge. The
optional Gauge
display shows one
channel of data in a
gauge/dial indicator
format.
The Gauge displays as
a separate window,
viewed simultaneously
with graph and other
windows.
NOTE: The Gauge feature is available in AcqKnowledge 4.2 and higher only.
The Gauge window:
- Will display one channel of data: (analog or calculation)
- Updates and displays simultaneously with the graph window. For analog channels only, the display will
update when the recording is stopped, but at a slower rate when recording is running.
- Can update during and in between acquisitions for all MP devices; display may be updated at a rate
slower than the sample rate and may display a value that represents the average of several samples.
- The background image (BMP, JPG or TIFF), indicator origin, range, length, thickness and color are all
user-configurable. An optional range band overlay can also be enabled.
- Selectable gauge bitmaps include Blood Pressure Cuff, BPM or Stopwatch
- All window preferences as well as the window visibility, size and position will be saved with the file.
- Window sizing is fixed to the size of the background image, meaning it will have a 1 to 1
correspondence with the monitor pixels

Gauge Preferences
Gauge Preferences are accessed by right-clicking over the gauge and using the
contextual menu. There are four tabs for setting the various Gauge parameters.

Background is the default tab presented in Gauge Preferences and contains options for setting the Background
image.
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Channel Provides a pop-up menu for assigning any one of the ENABLED analog or calculation
channels.
Background Image Displays the path and file name of the current background image. The default image is a
blue blood pressure gauge sized at 451 x 451 pixels.
Browse Allows alternative background images in different directories to be used in place of the
default gauges. The Browse location will default to the file path used by the currently
selected background image. To change the background image, click the Browse button
and locate the desired file. After the background image is specified, the pixel Width and
Height will be updated. The Width and Height fields are not editable.
Use Default Displays a menu of available default background images. (Pressure, Stopwatch and
BPM).
Indicator
The indicator or needle is a simple line vector drawn from an assigned center point to an endpoint
calculated according to the Length parameter. The indicator always rotates around the origin from low to high
values in a clockwise fashion.


Origin Is the center point of the indicator line referenced from
the top left of the image not the top left of the window meaning neither the frame of window
nor the title bar is included. The X parameter specifies the horizontal distance in pixels and
the Y parameter the vertical distance. X cannot exceed the Width of the background image
and Y cannot exceed the image Height. The default values are: Origin: X: Width/2, Y:
Height/2. Note that the pixel count starts at 0 so a 225 pixel square image will have its
center point at 112 pixels.
Visit the online support center at www.biopac.com
Part C Analysis Functions 227
Length Specifies indicator span in pixels starting from the Origin. Default is the smallest of the
Length or Width dimensions divided by 2.
Thickness Specifies the indicator width in pixels, with a selectable range between 1 and 10. The default is
1 pixel.
Color Specifies color of the indicator needle as Black (default) or White.
When recording is stopped
If the source channel is a Calculation channel, no gauge updating will occur when the recording
is stopped. Under this circumstance, the When recording is stopped options become
available. This allows the user to specify whether the indicator should not be displayed, should
be reset to zero, or should retain the last value.
Mapping
For setting up two point mapping: Input to Angle


Input Defines the input values in the scaled units. The units shown in the example are volts, but
would reflect the units of the source channel (mmHg, psi, etc.). The Input mapping of the upper
scale value is set to a default of 50 of the source channel unit type.
Angle Any angle can be entered, but 0, 360, 720, etc degrees means that the indicator will always be
pointing straight down.
When assigning mapping angles: Because the indicator needle must rotate clockwise, the
first value should be the lower angle. The first value also defines the indicators starting angle
but does not to need to be 0 degrees. For example, the Stopwatch Gauges starting angle should
be 180 degrees (pointing straight up). If half-circle gauges are used, the starting angle may be
90 degrees.
Indicator is limited to specific mapping
If this option is enabled, and the indicator needle reaches its mapped upper limit, it will stop
rotating and turn red. If this preference is not selected, the needle will not change color if the
defined mapping limits are exceeded and the needle will just continue in a clockwise rotation.
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Range Band (Default OFF)
Use the Range Band as an optional feature to highlight a specified area of the Gauge View.



Start/End Defines a pie shape (defined by Mapping values) sourced from Gauge center and
superimposed over the background image.
Color Clicking on the color bar will bring up the following palette, which allows any color to be
selected. The default color is green.

Opacity Used to adjust the transparency of the Range Band. 100% means the background image will be
fully obscured behind the range band, and 0% means the Range Band itself will not be visible.
The default setting is 50%.
Segment Timer Stopwatch option
(Available in AcqKnowledge 4.2 and higher only)
In addition to the standard Gauge described above, the Segment Timer Gauge option offers an analog
Stopwatch view of an acquisition in progress. As the recording progresses, a circular onscreen stopwatch
gauge displays the elapsed time with a sweep-second indicator. All customizable parameters shown above for
the default Gauge view are applicable to the Stopwatch view. A custom mapping for the Stopwatch view can be
created, or use the pre-configured Segment Timer Gauge graph template in the Sample Data folder.

Using the Segment Timer graph template open the sample template in the following directory:
Main drive\Program Data\Biopac Systems, Inc\AcqKnowledge 4.2\Sample Data\Segment Timer Gauge.gtl
Clicking Start will show the Stopwatch in progress. The template is setup to record ECG Lead II on CH 1 and
is tied to a new Segment Timer calculation channel. However, no connections are needed to verify the segment
timer and the template can be customized as desired. To change parameters, choose Preferences from right
contextual menu with mouse positioned over the gauge window.
Visit the online support center at www.biopac.com
Part C Analysis Functions 229
When the recording is stopped, timer indicator will also stop. When the next recording segment begins, the
segment timer will reset to 0. (This default can be changed in the Gauge Preferences).


To configure a new Segment Timer Stopwatch view:
1. Set up desired acquisition parameters and channels.
2. MP menu > Set Up Channels > Calculation tab and
choose the Segment Timer preset.
3. MP menu > Show Gauge and open Preferences by right-
clicking the contextual menu over the Gauge window.
4. In the Gauge Preferences, choose C0 Segment Timer
for the Channel and Stopwatch, as shown on right.
5. Choose the Mapping tab, enter the following Input to
Angle mapping values and click OK:

6. Start the acquisition. Note the Stopwatch view will accurately reflect the time scale of the recording
in progress.

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MP36R support
MP36R is a four channel data acquisition unit designed to work with AcqKnowledge for the research
market. AcqKnowledge 4 support for the MP36R unit includes:
Standard data acquisition and data acquisition features (triggering, multiple channels, variable sampling
rate, input values)
Output control functionality for controlling stimulators, digital channel, and channel redirection to
output
Standard analog presets for all SS series transducers
Electrode Check support
Multiple-MP device support. Similar to multiple MP150 support, each graph may acquire from a
maximum of one unique MP device.
Control channel support for changing digital output lines based on calculation channel analysis

Note AcqKnowledge software does not support MP36 units from the Biopac Student Lab product line
(without the R suffix for research systems).

Autoplot
Scroll
Both Autoplot and Scroll control how data appears on the screen. By default, AcqKnowledge displays the most
recently collected data first, and if more than one screen of data is to be collected, then the time scale will
scroll so that the newest data is always on the right edge of the screen.
When Scroll is deselected and Autoplot is checked, the screen will be cleared when the data reaches the right
edge of the screen, and plotting continues from the left again.
When both Scroll and Autoplot are unchecked, the incoming data will be plotted until the screen is full. Once
the screen is full, data will continue to be collected, but only the first screen is displayed. By default, the MP
will display the first eight seconds of the data record, but this can be reset manually by changing the horizontal
scale. To toggle Autoplot ON or OFF in the middle of an acquisition:
select Ctrl+T (Windows) or Command+T (Mac OS X) on the keyboard, or
pull down the MP menu and choose Autoplot ON or OFF

Warn on Overwrite
Selecting the Warn on overwrite option from the MP menu will generate a prompt each time you start a new
acquisition:

If you click Yes, then AcqKnowledge will erase your current file and overwrite with a new acquisition. If you
dont want to erase the file youre working in, click No and then open up a new file to work in.
This prompt will appear at the beginning of each acquisition when the MP System is in Repeating/Autosave
mode, so you will probably want to uncheck the Warn on Overwrite under the MP menu.
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Part C Analysis Functions 231
Organize Channel Presets

The Organize Channel Presets option controls the channel presets (established or new) in the MP > Set Up
Channels dialog; you can rename, rearrange or delete Presets. You might use this option to place the most
frequently selected Presets at the top of the menu or group related Presets, such as established ECG Presets and
new channel Presets youve created.
Click a Preset description to select it, and then use the buttons to organize the Presets.
Up and Down buttons move the selection one space at a time.
Top and Bottom buttons jump to the start or end of the list.
Rename a Preset by typing in a new description and clicking OK.
You cant use any name currently used by a Preset or any name that matches a Calculation type
(Integrate, Rate, etc.).

Delete a Preset by selecting that option. You cannot delete the Default Analog Input preset. When you delete a
Preset, you will be asked to confirm the request because it is an irreversible action.

Add Separator adds a new Separator entry to the Preset list and is useful for dividing different Preset types. If
a Preset is currently selected in the list, the Separator will be added below it. (See diagram above) If no preset is
selected, the separator will be added to the end of the list. Separators can be rearranged or deleted in the same
manner as Presets. (AcqKnowledge 4.2 and higher only)
The default location for Preset files is Computer > Local Disk > ProgramData > BIOPAC Systems, Inc >
AcqKnowledge 4.2 > Presets.

Exit Playback Mode
AcqKnowledge 4 Software Guide
This option is enabled when Open File for Playback (see page 42) has been selected. Select to resume
acquisition functionality (change Playback menu to MP menu, Replay button to Start button).

232 AcqKnowledge 4 Software Guide

Part CAnalysis Functions
OVERVIEW
This part describes how to analyze data; in most cases, analysis is performed after the data has been collected.
This involves creating, managing, and saving files, as well as editing data, performing mathematical
transformations, and displaying data in various ways. Many of the functions covered here are also discussed in
Part AGetting Started. Features that can be computed during an acquisition (primarily transformations and
calculations) are discussed in Part BAcquisition Functions.
For general information about sections of the graph window, and to become familiar with the look and feel of
AcqKnowledge, turn to the Editing and Analysis Features chapter. Descriptions of functions can be found in the
chapters describing each menu. All of the commands discussed here can be found under the File, Edit,
Transform, or Display menu items.

Menu See Type of Commands
File Page 233
General file management commands, including opening, saving, and
closing files. Export data files.
Edit Page 254 Cut, copy, and paste between and within files. Export data files.
Transform Page 264 Operations that primarily modify the data in the graph.
Analysis Page 295 Operations that primarily derive data and measurements from the graph.
Specialized Analysis Page 331
A courtesy copy of the new Specialized Analysis package with
automation and scoring routines is included under the Analysis menu.
Display Page 403
Control how data appears on the screen either during or after an
acquisition.
Media Page 431 Capture and Playback controls to synchronize video/audio with data.

Toolbars
Many of the most commonly used features in AcqKnowledge can easily be executed with a mouse click. The
toolbar contains shortcuts for some of the most frequently used AcqKnowledge commands; icons are grayed out
when they are not applicable.
Click Display > Show > Tool Bar to view the icons. Click an icon to activate it.
See page 54 for Toolbar icon definitions.

Shortcuts
Keyboard shortcuts are detailed on page 63.
Mouse shortcuts are detailed on page 67, including contextual menus.

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Part C Analysis Functions 233
Chapter 13 File Menu Commands
Overview

Most of the items in the File menu are standard menu items and follow the standard Windows conventions (for
MPWSW) or Macintosh conventions (for MPWS). By default, all files are created and saved in the
AcqKnowledge file format, a proprietary format used to store binary data. Data can be read in from either text
files or AcqKnowledge files, and can be saved in text, graphic, or binary format. As a rule, storing data in the
AcqKnowledge format saves information in the most compact format possible and takes up less disk space than
other file formats. In most cases, you will probably be working with graph windows and saving data in the
AcqKnowledge format.
AcqKnowledge also supports an online journal that can be used to store waveform data (in numeric format) or
to make notations and comments in a text file.
New
Graph Window
In almost all cases, you will need to create a new graph window before
beginning an acquisition so that the data may be displayed on the screen.
When a new graph window is created, you can modify any of the window
parameters, including horizontal scale, vertical scale, window size and
position. In addition, you can also set the acquisition parameters for
sampling rate, number of channels, and acquisition length. These settings
take effect once an acquisition begins.
New > Graph-specific Journal
Creates a graph-specific journal; see page 51 for details.

New > Independent Journal
Creates an independent journal; see page 51 for details.
New > Data View
Creates a new Data View for the active (frontmost) graph, and names the new window Data View of
Filename. . For Data View details, see page 43.
New > Batch Acquisition
Use the Batch Acquisition feature to configure advanced experimental setups and acquire data from a
sequence of templates. Each template in the Batch may have different acquisition settings, channel
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234 AcqKnowledge 4 Software Guide
configurations, and stimulator setups. Use a Batch for long duration experiments with hardware setting
changes across segments, to automate routines, or to run multiple experiments on the same experimental
setup in succession.
For example, if an experiment has a preparatory period, a stimulus period, and a response period, three
graph templates could be batched:
A template to acquire for the length of the preparatory period
A second template with a stimulator configured for the stimulus period
A third template to acquire the response period without stimulation
All three templates could be added in sequence to a single Batch Acquisition, which would then acquire all
of the data for all three templates with a single start.
To create a new batch, choose File > New > Batch Acquisition to generate the Batch dialog.
The Templates controls at the top allow you to add,
remove, or re-order the templates.
Double click a template in the list to open the
output graph from the most recent acquisition.
Batch acquisition cannot combine acquisitions that
do not end, so the acquisition storage mode for
template files cannot be set to Save last,
Autosave or Repeat forever.

Status
N/A No status is available for the template, no batch acquisition has been performed.
In Progress Data is currently being acquired for the template.
Waiting A batch acquisition is in progress but has not yet reached the step where the template is used.
Complete Data acquisition for the template has been finished successfully and has been saved to disk at
the batch output location.
Error A batch acquisition was aborted manually or due to communication errors. The data for the
template may not have been saved or may be unreliable.
Batch Errors
Misconfigured templates and misconfigured averaging templates may generate the Adjust
Length/Adjust Latency/Abort Acq warning prior to the start of acquisition. Clicking Abort
will halt the batch acquisition. Misconfigured templates may result in those rare cases where
data was acquired into a graph template with a different hardware configuration prior to saving
the template to disk.
Saving to:
Use the Change button to specify the
directory where the acquisition output should
be saved.

Use MP Unit:
Specify the MP150 unit that should be used for
the Batch Acquisition.
This menu lists all of the available hardware units.
Entire menu dimmed out while batch acquisitions are in
progress.
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Part C Analysis Functions 235

Start/Stop Acquisitions

Toggles to starts and stop batch acquisitions; dimmed
when the specified MP150 unit is being used to acquire
data unless it is a batch acquisition that is in progress.
Batch acquisitions may be terminated by using either a
control in the batch user interface or by clicking the
Stop button in the graph window actively acquiring
data for the current template of the batch. During the
execution of an individual template acquisition, errors
may occur that abnormally terminate that acquisition
(i.e., communications errors with the MP150 unit,
errors in calculation channel, disk errors, etc.). When
the acquisition in progress is terminated due to an error,
the batch acquisition will be halted as well.
If a batch acquisition is aborted early, the
batch output directory will contain the full
result graphs for all of the templates that
were previously completed successfully. It
will also contain a partial graph file for the
template that was being used at the time the
acquisition was aborted. Templates that
were not used will not have any associated
graph files.
Resume

When a batch acquisition is terminated prematurely, the
acquisition may be restarted from the first template in
the sequence or from where it was stopped (e.g. the
template with the error status).
Batch Acquisitions can be saved for use at a later time using File > Save Batch
Acquisition As. Batch Acquisition files retain all of the settings for their
individual templates and can be used even if the original templates used to
configure the batch no longer exist or have been moved. Each template is
acquired and saved into an output graph file that can be opened at a later point in
time to examine the results.
To open a Batch Acquisition, use File > Open and select type Batch
Acquisition.
When a batch acquisition is started, the templates will be executed in the order indicated in the batch to acquire
data from the specified MP150 unit. Files are autosaved before the next acquisition is started.
If the batch acquisition completes successfully, the batch output directory will contain all of the
graph files that were created during the acquisition. Each output graph is saved into a user-specified
directory and is titled Batch n - template name where n is the order in the acquisition sequence.
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236 AcqKnowledge 4 Software Guide
Open
The File > Open command generates the standard file open menu, and allows you to open a variety of different
file formats from the popup menu at the bottom of the dialog.

Multiple files
To open multiple files in a single dialog, hold the Shift key down and select multiple files. The Command-
A key combination will Select All files in the dialog. AcqKnowledge can only recognize one Journal file
at a time, so multiple selection is disabled when the file type is set to Journal or Journal Template.
Graph The default file formats (*.acq) is referred to as AcqKnowledge files. The
AcqKnowledge file format is the standard way of displaying waveforms in
AcqKnowledge. These files are stored in a compact format that retains information
about how the data was collected (i.e., for how long and at what rate) and takes
relatively little time to read in (compared to text files, for instance). AcqKnowledge files
are editable and can be modified and saved, or exported to other formats using the Save
as command. Format options for the graph file include
- GraphAcqKnowledge 4
- Windows AcqKnowledge 3 Graphprevious release format
- Macintosh AcqKnowledge 3previous release format
- Biopac Student Lab PRO Graphimport files created using the Biopac
Student Lab PRO software; to open BSL Lesson files (.ldd), manually add the
extension .acq to the end of the file.
BSL File Import Notes
BIOPAC produces two different software lines, the AcqKnowledge software
for research and the BSL software for higher education. These two
applications use different file formats, making it difficult to analyze data
recorded in one with the other.
AcqKnowledge can directly import data files that were created in Biopac
Student Lab PRO. This allows data acquired with an MP36, MP35 or MP30 to
be analyzed using the advanced analysis routines of AcqKnowledge.
Hardware and calculation channel settings are also imported. This allows for
the migration of some BSL PRO templates to AcqKnowledge. Only basic
analog, digital, and calculation channels can be acquired; templates that use
any of the BSLSTM or other output options are not supported.
Importing is limited to graph files created with BSL 3.6.6 or higher. It is not
possible to import files created with earlier versions of BSL. To import from
earlier BSL versions, those files must first be opened with BSL 3.6.6 or higher
and re-saved to disk to update the file format. The updated files can then be
imported directly into AcqKnowledge.
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Part C Analysis Functions 237

When saving files, AcqKnowledge must save using the AcqKnowledge graph
file format or another available export format. It is not possible to open
AcqKnowledge graph files with BSL Lessons or BSL PRO.
Template Graph Template files (*.GTL)
This powerful feature allows for creation of a template file with predefined experiment
parameters. Simply click Start to run the experiment.
The Graph Template option allows you to open a copy of a master file so you can
maintain the master settings. Graph template files open to previously saved setup
parameters (as established under the MP menu) primary graph window size.
This feature can be especially useful for recreating protocols in the laboratory. You can
Set Up an experiment and save it as a Graph template, then simply open the Graph
template file and click the Start button to acquire data under the same settings.
When a Graph template file is opened:
a) The graph window will not contain any data. (Since no data is saved in the
template, arbitrary waveform output setups, which require a source date file,
will not function in a template.)
b) The journal window will contain text you entered and saved with the
templatethis is a handy way for you to place instructions or information
about the experiment for yourself or others.
AcqKnowledge Quick Start (*.gtl graph template) files are available for over 40
applications. Just open the graph template file to establish appropriate settings for the
selected application, and then click Start. Quick Start files were installed to the Sample
Data folder and can be used to establish the settings required for a particular application
or as a good starting point for customized applications.
Text .TXT. Text files are a convenient way of transferring information between applications,
and most spreadsheet and statistics programs are capable of importing or exporting data
in a text file format. AcqKnowledge assumes that the text file contains numeric data laid
out in columns and rows, and that there is some delimiter between each column. It also
assumes that each column represents a distinct variable or channel of data. Normally,
the values in each row represent the state of each variable at different points in time.
When a text file is opened, the numeric values will be plotted as waveform data in a
standard graph window and non-numeric values will be ignored. Each column of data is
read in as a separate channel.
Journal *.JCQOpens an independent journal; see page 51 for details.
Open the journal file from the File Menu (File > Open > Journal); right-clicking or
double-clicking a saved Journal file will open a blank application window.
Jrnl
Temp
*.JTLOpens a journal template; see page 51 for details.
Options
When the Files of type: Text option is select, an Options button is activated. Clicking on
this button generates another dialog that allows you to control the amount and type of
data to be read in, as well as the time scale for data display.
N
O
T
E
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238 AcqKnowledge 4 Software Guide


Wave data starts on line
To control how much data is read in, enter a value in the read line box at the top of
the dialog. This tells AcqKnowledge which row contains the first data point in the
series. By default, this is set to 1, although you may want to set it to another value
since some applications (usually spreadsheets) generate a header, or text
information at the top of a file. You can also read in a limited amount of data by
entering a value in the box to the right of the line box. This value indicates the last
line to be read in as data. By default, text files will be read in starting at line one
and data will continue being read in until the end of the file is reached.
Interval
To control the horizontal scale (usually time) for the text file after it is displayed in
the graph window, change the Interval between sample points, which can be
expressed either in terms of time or frequency. For example, if data was collected
at 50 samples per second, there is an interval between sample points of 0.02
seconds. AcqKnowledge would then assume that there is a 0.02 second gap
between the data point in row two and the data point in row three (and all
subsequent pairs of adjacent rows). Likewise, if you have a data file that spans 10
seconds and has 100 rows of data, the interval between sample points will be 0.01
seconds.
Most files contain time domain data, although some applications generate
frequency domain data (the results of a spectral analysis, for example). The
principle here is the same as with time data, that there is some interval between
different frequencies. If a text file contains 20 sample points covering the range
between 0 and 60 Hz, then the interval would be set to 3Hz per sample.
Column Delimiter
This setting tells AcqKnowledge what characters indicate a gap between two
columns. This can be set to tab, comma, or space. All text files must have some
sort of column delimiter, unless there is only one channel of data present.
Tab delimited text files the most common type have a tab between each
column for every row of data. These files are most often generated by
spreadsheets and similar packages.
Comma delimited files place a comma between each column of data for each
row, much the same way as a tab delimited file. Statistics programs such as
BMDP and SAS frequently create these types of files.

Space delimited files are also commonly created by statistics packages, and
place some number of spaces (usually two) between each column of data for
every row which contains information.
None. If you are not sure which delimiter to use, select auto and AcqKnowledge
will automatically select a delimiter.
When either tab or comma is selected, AcqKnowledge will read in a new column
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Part C Analysis Functions 239
AcqKnowledge 4 Software Guide
each time it sees a delimiter, even if there are no numeric values between
delimiters. For example, the following text file will read in three channels of data,
although the channels will be of different lengths.
0.301424, 0.276737, 0.045015
0.338723, 0.808811, 0.542627
0.354271, 0.506313, 0.715995
0.001325, 0.762115
946207, 0.894992
0.926409,
Sample text file
The first channel will contain six data points, the first being 0.301424 and the last value
being 0.926409. The next channel will contain three data points, starting with 0.276737
and continuing through 0.506313. The software considers that there is no other data
values for channel two. The third channel starts with the entry 0.045015 and the last
data point for this channel is 0.894992. There are only five data points in the last
channel.
AVG Advanced Averaging Experimentnot supported in AcqKnowledge 4.0.
PhysioNet PhysioBank is a public service of PhysioNet and offers downloadable archives of
gigabytes of standard data for cardiac arrhythmias, gait analysis, and other types of
physiological signals. AcqKnowledge can use PhysioBank data directly and can be
integrated with other software tools that understand this interchange format.
A PhysioBank file is usually comprised of several files, including a header file (usually
*.hea), and all of the files must be located in the same directory for the PhysioBank
record to open successfully. Open using the header file.
Opening a PhysioNet file will import data and annotations into a new graph window. If
atruth annotations exist, they will be translated into appropriate events on the
appropriate channel. All annotation types are retained except LEARN annotations,
which are treated as UNKNOWN.
MAT MATLAB

format AcqKnowledge can open files created as a MATLAB



work space.
Windows can open MATLAB v6 compatible MAT files, including MATLAB 7
if the v6 flag is specified in MATLAB before saving.
Mac can open MATLAB v7 compatible MAT files, including V7 format. Only
ASCII text is supported; Unicode text within MATLAB v7 is not supported.
Interoperability with earlier versions of MATLAB is not guaranteed.
Uses the MAT-file binary format to load numerical and textual information. If the
MAT-file is properly formatted with the following arrays, AcqKnowledge will
reconstruct the graph with appropriate sampling rate, channel labels, units, and data:
data units labels isi isi_units start_sample
MATLAB

files open with no Start button.
If the MAT file is missing any of the
expected variables or contains extra
variables, only one two-dimensional array
variable can be imported into a graph. A
MATLAB Import Options dialog will be
generated. Choose which variable data is
stored in, what dimension maps to
samples, channel indices, and sample rate,
and then click OK to open the file.
If AcqKnowledge cant recognize the file
format, an error prompt will be generated
and a blank graph window will be opened.



240 AcqKnowledge 4 Software Guide
Raw
This low-level data exchange option interprets all data at a single sample rate; variable
sample rates are not supported. All of the data will be unscaled when opening
(importing) files. That is, a value of 0 will be imported as a zero voltage. Scaling will
need to be manually applied to the data. Options to open (import) raw data:
Data type: 32-bit or 64-bit IEEE floating point format or 8-, 16-, and 32-bit
integer formatted data
# of channels: Enter the number of channels stored in the data file as a positive
integer less than or equal to 60.
Layout: Packed sequential: All of the data for an individual file is located in
a single block of the file and multiple channels follow one another.
Interleaved: Data is grouped into a single frame for each sample
location with one data element for each channel, so data for a
particular channel is spread throughout the file (similar to Linear
PCM audio file format).
Endian: Little and big endian byte ordering, matching the data formats of x86
and PowerPC/Sparc, respectively. Set to big for Mac-Power PC
generated raw files (default), or to little for Mac-Intel generated or
Windows-generated raw files.
Set to x/sample: Specify the inter sample interval of data in the file, which will be
translated into an appropriate sampling rate. The edit field will
accept an arbitrary floating point number. The units menu contains
sec, msec, sec, MHz, kHz, Hz. The edit field will be dynamically
converted to match the units selection; no conversion will be used
when switching between frequency and time.
Batch Batch files (*bcq) is the format used for a saved Batch acquisition setup. All previous
configurations are saved in this file, so a Batch experiment can be rerun without having
to repeat the setup. When a saved Batch file is opened, the batch setup window appears
with previous graph templates intact. From here, the setup can modified and saved
under the same or a different name.
Igor Pro Igor Pro Experiments (compatible with Igor Pro 3.1, 4.0, and 5.0).
The waves contained in an Igor Pro packed experiment can be opened (imported) in
AcqKnowledge provided that the packed experiment files comply with the following:
59 waves
no text waves
no complex waves
all waves in Version 2 or Version 5 format (Igor defaults)
all waves one-dimensional (vectors)
all waves multiples of the same fundamental inter sample interval
If the wave has an associated wave note, it will be used as the channel label.
WAV
WAV files containing 60 channels or less can be imported. When this format is chosen,
the list of available files will be filtered such that only files ending in the .wav
extension or having the WAVE type are shown. When a WAV file is selected, it will
be analyzed to determine if it is compatible with the AcqKnowledge application.
If the file is compatible, a new graph window will be created displaying the data
contents of the WAV file.
- Each channel will be numbered Channel n where n is an increasing digit.
These channels will be unitless in amplitude.
- All of the data will be converted into the 64 bit floating point format for storage
in memory and in the ACQ formatted files on disk.
- The horizontal axis of this graph will be set to time and the sampling rate set to
match the rate as specified in the WAV file headers.
- This graph will be marked as an imported graph into which data cannot be
acquired.

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Part C Analysis Functions 241
- This will dim the start button and any appropriate hardware menu entries that
would be used to access the invalid hardware settings.
EDF
Opens files with .eeg and .edf extensions saved in European Data Format (EDF). Data is
imported entirely into memory in a newly created graph window titled after the
filename, similar to other file import routines. All scaling factors will be applied to the
data as it is imported, and it will be converted to double precision floating point format.
Since EDF format includes data that is not used by AcqKnowledge, only the following
items are imported:
- channel data
- channel labels
- units
- sampling rate (taken from maximum sample rate of all channels)
All other information stored in the EDF file will be discarded when the file is imported.
Only 60 channels of data can be imported from an EDF file. Channels will be imported
starting with the graph file index 1. If there is a 60th channel, it will be placed into the
channel with index 0. If an EDF file contains more than 60 channels, only the first 60
channels will be imported and a prompt will advise that not all of the channels could be
imported.

Open Recent
The File > Open Recent command generates a list of recently used files. These files can be opened directly from
the list or with a Ctrl (PC) or Command (Mac) keystroke combination. (File > Open Recent is available in
AcqKnowledge 4.2 and higher).

The listed files appear in the order they were opened, with the most recently-opened file appearing at the top.
Default number of files appearing in the list can be modified in the Preferences. (Display > Preferences >Other)
Open for Playback
The File > Open for Playback command generates a standard file open dialog; see page 42 for Playback details.
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242 AcqKnowledge 4 Software Guide
SMI BeGaze Import
Allows for import of SensoMotoric Instruments BeGaze eye tracking data and aligns the data with signals
recorded in AcqKnowledge. In order to use the BeGaze SMI Import feature in AcqKnowledge, the BeGaze eye
tracking data must first be exported to a text file format that AcqKnowledge can read. (BeGaze software offers
text file export of the eye position, pupil width measurements, and analyzed data.) Eye tracking data can be
imported into an existing AcqKnowledge graph, a new graph, or aligned to existing data. (See BeGaze Import
options below.)
To use TTL display trigger synchronization, the digital output line from the SMI hardware must be connected to
the MP unit used to record data and must be enabled during data acquisition. The time of the first image
presentation within the BeGaze data will be placed at the first positive peak in the digital signal. The softwares
timestamp alignment will attempt to extract the recording time from the BeGaze data and align it with the
internal AcqKnowledge timestamps. Software timestamp alignment is functional only with newer versions
of BeGaze.
When importing and aligning data to an existing graph, the physiological data must be recorded into a single
segment. Data recorded as multiple appended segments will not be properly aligned.
BeGaze exports may contain only a subset of the recorded and analyzed data. If a signal is not present in the
export file, its checkbox will be removed from the available signal types in the 'Signals to import' lists.
Note: The SMI Begaze Import feature is available in AcqKnowledge 4.3 and higher only.

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Part C Analysis Functions 243
Close
This File menu command will close the active file window and prompt you to save if necessary.

Close without saving
Windowsclick the in the upper right corner of the file window
Mac OS Xclick the in the upper left corner of the file window
Click No when AcqKnowledge asks you if you want to save the changes.
Close during acquisition

Close multiple data views
Set the level of close functionality under Display > Preferences > General.

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244 AcqKnowledge 4 Software Guide
Save

This menu command will save any changes made to a file. If more than one file is open, this command only
applies to the active window. For untitled files, you will be prompted to name the file you wish the data to be
saved in. The file will remain open after you have saved it, allowing you to continue working.
- The Save menu is dynamic and corresponds to the type of file you are trying to save, i.e. Save Graph,
Save Journal.
Files should be less than 2 GB, except AcqKnowledge 3.9 Graph files on the Mac, which can be larger if not
compressed. Data files greater than 2GB can be opened, but edit, transformation and analysis operation cannot
be performed.
To save data in another format (such as a text file), use File > Save As.

Save As
Choosing File > Save As produces a standard dialog that allows you to
save data in a variety of different formats and to any location. As with all
save last dialogs, you can use this to save a file to a different file name or
directory than the default settings.


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Part C Analysis Functions 245
Graph
AcqKnowledge format
The default file format for the File > Save as command is to save files as an
AcqKnowledge 4.0 file, which is designed to be as compact as possible. These files can
only be opened by AcqKnowledge 4.0, but data can be exported to other formats once
it has been read in.
- To save in the previous release format, choose Windows AcqKnowledge 3
Graph. When a file is saved in AcqKnowledge 3 format, the following
calculation channel types will revert to Integrate: Band Stop Comb Filter,
Adaptive Filter, FLC, WFLC, CWFLC, Rescale and Metachannels.
File Compatibility
Windows AcqKnowledge cannot save as Macintosh AcqKnowledge files.
Macintosh AcqKnowledge 3.9 and above can save as Graph (Windows) files, but it
saves in Windows AcqKnowledge 3.7.1 format. In this earlier format, all data is
retained, but new Windows AcqKnowledge features (like dual stimulation, data
views, embedded archives, etc.) are lost along with any settings specific to Macintosh
AcqKnowledge (like events, adaptive scaling settings, etc.).
Macintosh AcqKnowledge 3.9 and above can save PC-compatible Graph (*.acq)
and Graph Template (*.gtl) files. Variable sampling rate information and
hardware settings are retained, and Journals can be read from and written to PC
files. Choose the format Graph (Windows) to create PC-compatible files.
The Mac version does not save PC GLP files or compressed PC files.
Files must end on a multiple of the lowest channel sampling rate to be fully PC
compatible.
GTL Graph Template
This feature can be especially useful for recreating protocols in the laboratory. You
can Set Up an experiment and save it as a Graph template, then simply open the Graph
template file and click the Start button to acquire data under the same settings.
TIP: Check the existing Quick Start template files listed on page 237 before
creating or saving a new template. With over 40 templates provided, you
may find one to establish the settings required for your particular
application or to use as a good starting point for customized applications.
The Save As Graph template option saves the setup parameters established under the
hardware menu and retains the size of the primary graph window. In general, the
minimum file size for graph templates is 700 K-800 K; file size may increase as setup
options are enabled.
When a file is saved as a Graph Template:
a) No graph data will be saved.
- Since no data is saved in the template, arbitrary waveform output
setups, which require a source date file, will not function in a
template.
- You must select Save / Save as and select File of type .ACQ to
save the graph data.
b) Journal text will be preserved. Any text you entered will be saved to the
Journal window and stored with the templatethis is a handy way for
you to place instructions or information about the experiment for yourself
or others.
When this feature is used with the menu.dsc customization feature it is easy to comply
with GLP standards and save your protocol as an SOP. When you change the menu.dsc
file for a graph template file, save the menu.dsc file with the exact same name but
save it to the new lesson folder you have created. For full GLP features, contact
N
O
T
E
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246 AcqKnowledge 4 Software Guide
BIOPAC about the Lab Assistant GLP System.
TXT Text
Saves graph data in text format. When Save As Text is selected, an Options button is
generated. Clicking on this button generates a Save Options dialog that allows you to
control how much data is saved and the format it is saved in.

Include header
When the first box is checked, a header is included at the top of the text file that
contains information about the sampling rate, number of channels, date created, and
other information relating to the data. This information is frequently useful, but some
programs will attempt to read in the header information as data, which could result in
nonsensical results. You may wish to include the header as it can always be edited
out later using a text editor or the journal.
Horizontal Scale
The second checkbox allows you to include the horizontal scale (usually time) values
in the text file, along with the data to be saved. This allows you to produce time
series plots in other applications, as well as correlating events to time indexes in
graphing and statistical packages. Since a separate row is generated for each sample
point, To exceed the limitations of programs if data is collected at a fast sampling
rate (many spreadsheet programs are limited to about 16,000 rows). You may wish to
consult the section on resampling data after an acquisition is completed (page 291 ).
Delimiter
When data is saved as a text file, each channel of data is saved as a separate column,
with the number values for each data point saved in rows. Use the pop-up menu to
select the delimiter to separate the columns of data in the text file. By default, a tab is
placed between each column for every row of data; this format is called a tab-
delimited text file and almost all applications will read in tab-delimited text files.
However, you may also save data in a comma-delimited format or a space-delimited
format.
Line ending
Use to create text files that are compatible with Classic Mac OS applications (Mac),
Unix-compatible applications (Unix), or PC-compatible applications (DOS).
Precision
Use to define the number of significant digits used for the horizontal scale when
pasting wave data. Very high sampling rates may require more than the default value
of 6 digits to accurately resolve the inter-sample interval.
PhysioNet This format requires that the WFDB library is on your computer. PhysioBank is a public
service of PhysioNet and offers downloadable archives of gigabytes of standard data
for cardiac arrhythmias, gait analysis, and other types of physiological signals.
AcqKnowledge can use PhysioBank data directly and can be integrated with other
software tools that understand this interchange format.
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Part C Analysis Functions 247
AcqKnowledge 4 Software Guide

Saving a file in PhysioNet (WFDB) format will export the entire contents of the graph
to a PhysioBank record. The record will consist of multiple files, all in the location
specified for export. There will be a header file (*.hea) and a single data file for each
channel of the graph (starting with d and ending with the base name of the header
file). The files must not be separated for a successful move or copy.
Export Limitations
Precision Some precision may be lost due to differences in binary representation
between AcqKnowledge and PhysioBank formats.
Events Events will not be exported to the PhysioNet format.
Channels Only 32 channels of data can be exported from a graph (the max allowed
in a PhysioBank file).
Rate If you are exporting a graph that uses variable sampling rates, all of the
channels in the exported file will be downsampled to the lowest waveform
sampling rate of the source graph.
*.MAT
MATLAB
MATLAB

format. Uses the MAT-file binary format to save numerical and textual
information as Filename.mat.
Windows and Mac create MATLAB Version 6 files, which are compatible
with both MATLAB Version 6 and MATLAB Version 7.
Interoperability with earlier versions of MATLAB is not guaranteed.
The following variables will be in the workspace when the file is opened in MatLab.
data Contains the data of the graph in floating point format, for all of the
channels of the array. The first dimension of this array is the amount of data
in each channel, the second dimension increments with each channel.
Therefore, each column contains a full channel of data that can be accessed
in MATLAB via data (1:length, [channel number]).
units This string array contains the textual representation of the units of the
samples stored in data, with one element per channel of data.
labels This string array contains the labels of each of the channels, with one
element per channel.
isi This floating point array of one element gives the number of units of a
single inter sample interval of the data.
isi_units This single string array provides a units string for a single unit of isi. Time
data will always be ms, frequency data will always be kHz, and other
values will be represented by an Arbitrary horizontal axis type in an ACQ
graph.
start_sample Contains the time offset of the index 0 sample of data in isi units. This will
be 0 for many graphs, but if only a selected area of a graph was exported
into the MAT file, the start_sample will contain the offset from the original
data corresponding to the start of the data array in the MAT file.
Raw Options to save (export) data for low-level data exchange are:
Data type: 32-bit or 64-bit IEEE floating point
Layout: Packed sequential: All of the data for an individual file is located in a
single block of the file and multiple channels follow one another.
Interleaved: Data is grouped into a single frame for each sample
location with one data element for each channel, so data for a particular
channel is spread throughout the file (similar to Linear PCM audio file
format).
Endian: Little and big endian byte ordering match x86 and PowerPC/Sparc data
formats, respectively. To exchange with Windows applications or Mac-
Intel, set to little endian; to exchange with standard Mac applications, set

248 AcqKnowledge 4 Software Guide
to big endian.

Raw Data Export Limitations
Formats Raw export only allows data to be saved in 32-bit and 64-bit IEEE floating
point format.
Rates All files will be interpreted at a single sample rate; variable sample rates
are not supported. If a graph with variable sampling rates is exported,
channel data for downloaded channels will be padded to match the highest
waveform sampling rate.
Length If channels have unequal lengths, the overall file length will match the
longest channel. Shorter channels will be padded at the end using their
final sample value so that all channels contained in exported files will be
equal in length.
Scaling When integer-valued analog channels are exported from AcqKnowledge to
raw files, all relevant scaling and offset will be appliedthe data in the file
will appear the same as if the channel had been internally converted to
floating point format before export.
If the value of a channel is outside the maximum/minimum value that a
chosen export data type can represent, the value will be clipped
accordingly. (AcqKnowledge uses a 64-bit data type, so this should only be
a problem if exporting to 32-bit floating point values.)
Igor Pro Igor Pro Experiment format.
An AcqKnowledge graph will be saved (exported) to a single packed experiment file,
with each channel saved into a separate Igor wave that preserves the channel label,
waveform sampling rate, and unit information. Vertical units will be stored as data units,
and horizontal units will be stored dimension units; extended units are supported. The
scaling of each wave will be adjusted to match the waveform sampling rate. All data
will be stored in 64-bit floating point format in a one-dimensional wave. The waves will
be named incrementally from wave0 and the channel label will be stored in the wave
note field. Files will have the type/creator pair IgsU/IGRO and a .pxp extension will
be added to the file name for compatibility with Igor Pro for Windows.
WAV
This option saves the graph data into a WAV audio file for exchange with other
applications. The .wav extension will automatically be added if the save as filename
does not end with it.
The Selected area only checkbox will be active for WAV export. When checked, only
the highlighted area will be exported to the WAV file. The final sample of this range is
not included in the export, mirroring the other file export routines of AcqKnowledge.
All exported WAV files use the 64 bit floating point format. This format preserves full
operational precision. Most audio applications should be able to support floating point
WAV files. Exported data will not be normalized when it is exported. Any
normalization to audio ranges should be performed prior to exporting the data.
WAV files are normally either one or two channels (e.g. mono or stereo).
AcqKnowledge graph files, however, usually contain more than two channels. Although
they can contain more than two channels, most audio applications may not be able to
recognize these multiple channel files.
- If a graph file contains only one or two channels of data, a WAV file will
automatically be created without further interaction.
o Graphs with a single channel will result in mono WAV files.
o Graphs with two channels will result in stereo WAV files.
- If a graph contains more than two channels, the user will be presented with the
following choice:
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Part C Analysis Functions 249

o all channelscreate a multiple-channel WAV file with one channel per
channel of data in the graph. While this WAV file may be easily opened
by some applications, it may not be fully compatible with audio
applications and other applications expecting two channels or less.
o selected channel onlycreate a single channel mono WAV file using
only the data of the selected channel. This will be the selected channel
in chart mode, the active channel in scope mode, or the vertical channel
in X/Y mode. This single channel export may be useful for exporting
audio channels that are recorded along with physiological data, such as
heart sounds, audio stimuli, and the like.
After a WAV file is exported, the WAV file will not be reopened; the open graph will
be left unmodified. To view the exported file, import the WAV file.
EDF Saves file in European Data Format (EDF). The saved file will automatically have an
.edf extension added onto it if the user did not include it. Users will be able to save
either the entire graph or only a selected portion of data.
AcqKnowledge does not retain sufficient information to accurately complete an EDF
header. When exporting, the following default values will be used:
EDF Header Element Default
subject ID Empty*
recording ID Empty*
recording date Set to the modification date of the graph file on disk.
If no graph file is on disk, the current date is used.
recording time Set to the modification time of the graph file on disk.
If no graph file is on disk, the current time is used.
transducer description Empty*
filter description Empty*
* Empty: indicates that the field will be left blank
All other fields will be filled with corresponding information from the graph, including
channel titles, sampling rates, channel units, and scaling factors. Variable sampling rate
information will be preserved as it can be expressed in the EDF format.
EDF is used by many applications and online recording databases to store information,
particularly EEG recordings. EDF is an open file format originally developed for sleep
studies. It stores continuous time recordings of data in a binary format. Since its original
proposal, EDF has been adopted by a number of open source and commercial tools as a
supported data file format. Usage has also expanded beyond sleep studies into other
types of recording.
JPG
AcqKnowledge also supports formats for saving graphical information. Most drawing,
page layout, and word processing programs can read .JPG files. This is particularly
useful for writing reports. A. JPG file can be opened in any standard drawing program
and can then be embellished or used to highlight any particular phenomena of interest.
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250 AcqKnowledge 4 Software Guide
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When data is saved as a graphic, only the data currently on the screen is saved. So, if
you have a data file that spans eight hours but only two minutes is displayed on the
screen, only two minutes of data will be converted to a graphic file. Since
AcqKnowledge uses information about the computer screen in creating the graphic file,
the default resolution of the file will be the same as the window. Most word processors
and graphics packages allow for some way to resize and scale graphics.
Compressed Saves a compressed AcqKnowledge formatted file. The degree of compression varies
based on data characteristics, but will generally achieve about 60% compression. Saving
small files (less than 200K) may have little effect. Using a sample file as an example:

Compressed graphs no longer allow data acquisition and will open with no Start button.
A warning prompt will be
generated when you try to
compress a graph in which
data can be acquired (Start
button active):
Excel
Spread-
sheet
Excel Spreadsheet ExportGraph data can be saved directly to an Excel spreadsheet by
using the Excel Spreadsheet format in File > Save As. Each channel will be placed into
its own column of the spreadsheet. Only 65K sample points can be exported at a time,
however, so long or high sample rate data acquisitions may not be able to be saved in a
single spreadsheet.
- Also available for File > Save Journal Text As, Find All Cycles journal, and
Specialized Analysis tools.
Note The Excel spreadsheet option requires Excel or a compatible spreadsheet
application that can read Excel files (OOo, Symphony, etc.). If Analysis results
are exported to an Excel spreadsheet, and a compatible application is not
available, results will open as a text document the data and nonsense characters.
Save Selection As
To save only the data that has been selected with the I-beam tool, choose File >
Save Selection As; this option saves the selected area to another file and does
not affect the current file that you are working in. Specify file name and file
type and then click Save.

Visit the online support center at www.biopac.com
Part C Analysis Functions 251
Save Journal Text As

Choosing File > Save Journal generates a save dialog to save the journal text as a separate file. Specify file
name and file type and then click Save.
Journal

Text (*.TXT) formatSaves an independent journal; see page 51 for details.
Jrnl
Temp
.JTL formatSaves a journal template; see page 51 for details.
Excel
Spread-
sheet
Excel Spreadsheet File (*.XLS)Journal text can be exported directly into an Excel
spreadsheet by using the File > Save Journal Text As with the Excel Spreadsheet format. Each
line of text in the journal will be saved as a single row with tabs separating columns. A
selected portion of a journal can also be written to a spreadsheet. This export allows for textual
data reduction results to be easily exported into a spreadsheet to allow for further analysis.
- Also available for File > Save As, Find All Cycles journal, and, for Specialized
Analysis tools.
Note The Excel spreadsheet option requires Excel or a compatible spreadsheet application
that can read Excel files (OOo, Symphony, etc.). If Analysis results are exported to an
Excel spreadsheet, and a compatible application is not available, results will open as a
text document the data and nonsense characters.

File Format prompts
When a file open or save function requires a format change for compatibility or alters file content, a prompt will
be generated to require the user to confirm the option to update format or convert and save.


Created with a previous version of AcqKnowledge Windows PC AcqKnowledge format


Saving as a Graph Template will erase all data Imported from another file format
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252 AcqKnowledge 4 Software Guide
Send Email Attachment
Use this feature to create an email attachment containing an image of the active AcqKnowledge graph, along
with the journal contents. (AcqKnowledge 4.2 and higher only).
When using this feature:
o The default email program will launch, along with a compose new email window.
o An Open Document (*.odt) text file containing an image of the currently opened graph and associated
journal text will be copied to the attachment field. The formatting and images present in the journal
should be preserved.
o Further details can be typed into the body of the email prior to sending.
In order to open the attachment, the email recipient must have a word processing application compatible with
*.odt file format, such as OpenOffice, NeoOffice or Microsoft Word

.

Page setup
Choosing File > Page Setup produces a standard printer setup dialog that allows you to setup any available
printers. All the options in this dialog function as described in your system manual. There is also an options
button that allows you to make several printing adjustments with respect to fonts, image orientation, and
graphics presentation.
Print
The File > Print menu that AcqKnowledge uses is similar to the standard computer print dialog; however, there
are additional options available
The Print menu is dynamic and corresponds to the type of
file you are trying to print, i.e. Print Graph, Print Journal.
Click Print for more options.
Note: In Mac OS X, the option to create a PDF file appears
in the initial Print dialog.


- Print Options
Plots per pageControl how many plots appear per page when the file is printed. Printing more than
one plot per page has the effect of snaking graphs on a page much the same way text appears in a
newspaper. For example, if this option was selected so that two plots were printed per page,
AcqKnowledge would divide the amount of data to be printed on that page into two graphsone graph
printing at the top of the page, the second graph printing at the bottom of the page. This option allows
you to print records on considerably fewer pages than standard printouts, and is most effective when
only a few channels of data are being printed.
Fit to pagesPrint the contents of a window across multiple pages. When a record is printed over
multiple pages, the amount of data on the screen (the amount of data to be printed) is divided by the
number of pages entered in the dialog. The graph on the screen is then printed across the number of
pages specified in the Total pages box at the bottom of the File > Print dialog. These two options apply
only to graph windows, and do not apply to Journals.
Visit the online support center at www.biopac.com
Part C Analysis Functions 253
- Draw vertical dividers at event positionsAdds visible borders at points where events occur.
- Print waveform data in blackWaveforms will appear black when printed, regardless of selected colors
in graph channels.
- Print waveform background in whitePrints white background, regardless of selected background
colors in graph channels.
- Print focus areasTurns focus areas on or off for the printout.
- Range Optionsdetermine the range of data that will be included in the printout
Visible portion only synchronizes the range of data in the printout to match the range of data that is
visible on the screen.
Selected portion only prints only the data that is selected in the graph. This option is disabled if there is
no selection in the graph. When working with Journals, it is easy to generate large amounts of text
content in the window. Only a portion of this information may actually be of interest and this feature
allows for only portions of the text to be printed. If there is no selected text, the entire journal or
modification log will be printed regardless of this setting.
Entire graph prints all of the data contained in the graph from zero to the maximum length channel.
- Print to PDF filegenerate a PDF file.
Quit
Select Quit from the File menu to exit AcqKnowledge software; you will be prompted to save any open
graph files that have been modified since they were last saved.
Mac OS X onlyUse Quit under the AcqKnowledge menu (page 429) to exit the software.
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254 AcqKnowledge 4 Software Guide
Chapter 14 Edit menu commands
Overview


One of the most useful features in AcqKnowledge is the ability to edit and work with data by cutting sections
and copying sections from one window to another. In this sense, the MP System (MP150 or MP36R) allows you
to work with data much as a word processor lets you work with text. When working with data, you will usually
want to select a section of data to work with. To select a section of data, use the editing tool to highlight an area.
The selection tool is used for a variety of purposes including cutting and pasting waveform data, making
measurements and determining which portion of a waveform to save as text values. To select the tool, click its
icon in the lower right hand corner. You will notice that the cursor changes into the familiar I-beam cursor
when you move it within the graph area. Click the mouse and drag to select a portion of the waveform.
IMPORTANT
When multiple waveforms are present, the highlighted area appears to include all of the waveforms,
but most modifications and transformations apply only to the selected channel.
Once you have selected a section of a waveform, you can perform such as editing, transformations, saving data
to the journal, saving as text, and using the measurement functions on the selected area. The cursor always
selects at least one sample point; when there is no defined area, a single sample point will be selected, and the
cursor will blink. You can highlight a larger area by positioning the cursor over the first point you are interested
in, holding down the mouse button, and dragging the cursor either left or right to highlight an area. This is
similar to highlighting a series of letters or words in a word processor. You can modify the selected area by
placing the cursor anywhere on the graph, then holding down the shift key and clicking the mouse. This feature
is useful for fine-tuning the selected area. To fine tune, first coarsely select an area. By zooming in (with the
zoom tool) on either edge, you can then use the shift key to precisely align the edges of the selected area.
AcqKnowledge also allows you to select an area that spans multiple screens. To do this, first select an area that
contains the leading edge of the portion of the graph that you are interested in. Next, use the horizontal scroll
bar to scroll to the end of the area that you are interested in. Then place the mouse near the area of interest and
click the button while holding down the shift key. While still depressing the mouse button, move the cursor to
the exact position desired.
By using the selection tool to select areas of the waveform, the Cut, Copy, Paste and Clear functions are
designed to work in much the same manner as a word processor. These functions operate only on areas selected
by the selection tool.
Visit the online support center at www.biopac.com
Part C Analysis Functions 255
Edit menu functionality during acquisition
The following Edit menu functions may move or alter memory and cannot be performed during acquisition:
Undo, Cut, Clear, Clear All, Paste, Insert Waveform, Duplicate waveform, and Remove Waveform.

Undo / Cant undo
The Undo command allows you to restore data that was unintentionally deleted or modified. Undo applies to
editing commands and transformations (such as digital filtering and mathematical operations).
There are some important exceptions to the Undo command.
First, neither Edit > Clear all nor Edit > Remove waveform can be undone. It is a good idea to make backup
files before performing any editing, especially when using these commands.
Second, changes in the display options (i.e., changing the horizontal scale or changing the color of a waveform)
cannot be undone, since they are easier to manipulate and less drastic than cutting data out of a waveform. If
you modify the screen scale (or other display parameters) you will still be able to undo your latest data
modification, which is much more difficult to recover than a screen parameter change.
TIP: If you accidentally remove a waveform or choose Clear All, one way to recover
the data is to close the file without saving the changes. The data file can now be
reopened, as it was when it was last saved; any changes made since it was last
saved will be lost.
Perform multiple levels of undo on a per graph basis; Journal undo remains unchanged at one step. Complex
data analysis in AcqKnowledge is rarely performed with a single transformation; multiple transformations are
frequently cascaded together to produce a result. AcqKnowledge will stack the transformations and the user
will be able to undo one step at a time until this stack is exhausted.
- Undo may move or alter memory and cannot be performed during acquisition.
- Undo operations may occupy large amounts of memory, particularly for transformations that affect
entire waveforms or multiple events. Users without large amounts of RAM or working with large data
sets may require the available computer memory for performing transformations. To accommodate
these users, the maximum size of the undo stack can be limited using the Levels of undo Preference
(Display > Preferences).

- Specialized Analysis (page 331) scripts are complex and undo may not function for all steps.
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256 AcqKnowledge 4 Software Guide
Cut
When Cut is selected from the Edit menu, the highlighted portion of the active window (Graph, Journal, entry
prompt or dialog) is removed and copied to a clipboard, where it is available for pasting into other windows.
Cut may move or alter memory and cannot be performed during acquisition.
When a selected area is removed from a waveform, the data will shift left to fill in the deleted area. So,
if ten sample points are deleted, all data after the selected area will be shifted over ten sample points.
Since this alters the relationship of events to the time base, you might want to consider alternatives to
cutting sections of datasuch as using smoothing, digital filtering, or the connect endpoints functions to
transform the section of data.
Area selected using the
editing tool






Same data with selected
area Cut out

Note that the data
after the selected
area has shifted
forward in time.


Copy
Choosing Edit > Copy will copy the selected area of the active window (Graph, Journal, entry prompt or dialog)
to the clipboard without modifying the text/waveform on the screen.
Once the area has been copied, it can be inserted in another window using the Edit > Paste command or,
for waveforms, the Edit > Insert waveform command.
To copy a waveform to another channel in the same graph window, choose the Edit > Duplicate
waveform command.
Paste
The Edit > Paste command will take the contents of the clipboard and paste it into the currently selected area of
the active window (Graph, Journal, entry prompt or dialog).
If no area is selected, the data is pasted at the beginning of the waveform in a Graph window or the end of
the text a Journal window

Note Copy/Paste operations require AcqKnowledge to allocate additional memory and then load the data into
memory; when these operations are executed on large data files, the application may crash.

Visit the online support center at www.biopac.com
Part C Analysis Functions 257
Clear
The Edit > Clear command works much the same way as the Cut command, with the key difference being that
data is not copied to the clipboard. This function deletes the selected area from the selected channel only. If the
entire waveform is selected (as with the Edit > Select all command), the clear command will delete all the
waveform data and leave an empty channel.
Clear may move or alter memory and cannot be performed during acquisition.
As with the cut command, the clear function operates on only one channel, and when a portion of the
waveform is deleted, the remaining data will shift left. If multiple channels of data are present, one
channel will be shorter than the others.
To remove a selected area of data from multiple channels, use the Edit > Clear all command.

Clear all
Choosing Edit > Clear all will delete the selected area from all channels. This is similar to the clear function in
that data is removed and is not copied to the clipboard. The Clear all command, however, removes a section of
data from all waveforms, whereas the clear command applies only to the selected channel.
Clear All may move or alter memory and cannot be performed during acquisition.
When Edit > Select all is chosen prior to performing the Clear all function, all waveform data for all
channels will be deleted.
The Edit > Undo command does not work for Clear all.

Select All
When Select all is chosen from the Edit menu, the entire selected channel becomes highlighted. For almost all
commands, when a waveform is selected using Select all, subsequent operations apply to the selected channel
only.
The exception is when Edit > Clear all is chosen after Edit > Select all. When this occurs, all data from
all waveforms will be deleted.

Insert waveform
The Edit > Insert waveform command is useful for copying a waveform (or a section of a waveform) from one
window to another. To do this, first select the area to be copied using the cursor and the Edit > Copy command.
Next open the graph window you wish to insert the waveform into. To insert the waveform into the same graph
it was copied from, although the Edit > Duplicate waveform is a much more straightforward way to do this.
Once you have selected the graph you wish to insert the waveform into, choose Insert waveform from the Edit
menu. A new (empty) channel will then be created and the data will be copied into the empty channel. The new
channel will always take on the lowest channel number available (including zero).
Insert waveform may move or alter memory and cannot be performed during acquisition.
This command cannot be undone directly, although selecting the inserted channel and choosing Remove
waveform from the Edit menu effectively undoes this operation.
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258 AcqKnowledge 4 Software Guide
Duplicate waveform
Choosing Edit > Duplicate waveform will create a new channel in a graph window and copy an entire
waveform (or a selected area) to the new channel. When a portion of the waveform is selected, only the
highlighted area will be duplicated.
Duplicate waveform may move or alter memory and cannot be performed during acquisition.
To duplicate the entire waveform, choose Edit > Select all and then select Duplicate from the Edit menu
or click the right mouse button and select Duplicate from the pull-down menu.

Remove waveform
Deletes the entire selected waveform, regardless of what other options are selected. Remove waveform may
move or alter memory and cannot be performed during acquisition.
The Edit > Undo command does not work for Remove waveform.

Remove last appended segment
Removes the last appended segment. Equivalent to the Rewind toolbar icon.

Edit > Undo does not work for Remove last appended segment.

Create Data Snapshot
The Snapshot options store snapshots of the original acquired data at specific stages along with the full graph
file. Use snapshots for analysis or reporting to compare results to original waveforms or intermediate stages of
analysis. This is essentially an embedded archive; it is not a backup tool.
IMPORTANT: Archive functions do not create a new filethey are not backup functions.
Original data is copied and pasted to the end of the original file.
You cannot use this feature to recover lost or damaged graph files.
See page 52 for Snapshot details.

Visit the online support center at www.biopac.com
Part C Analysis Functions 259
Merge Graphs
Combine multiple graph files into a single file for performing cross-file analysis and storage. Use merge with
the multiple-hardware capabilities to produce single graph files containing multiple streams of data from an
individual subject.
Use Merge Graphs to combine up to 60 channels from multiple graph files acquired with the same acquisition
rate into one merged graph file.

Note Merge Graphs requires AcqKnowledge to allocate additional memory and then load the data into
memory; when this operation is executed on large data files, the application may crashon Windows
OS, the resulting file size of a merge should be less than 2GB; data files greater than 2GB can be
opened, but edit, transformation and analysis operation cannot be performed.

1. Select Edit > Merge Graphs to generate the Merge Graphs dialog.
2. Click Add Graph to generate the Choose Graph dialog.
3. Choose a file to add to the merge.
Add the Matching graph listed (this pull-down menu includes all open files with the same
acquisition rate)
Add File to browse and select a file that is not already open
4. Adjust the selection for individual channels if desired.
Click the + to list individual channels in the graph file.
Toggle the checkbox to add or remove the associated channel/graph file.
You cannot delete a file name from the list, but you can remove it from the merge.
5. Repeat as desired for multiple files.
6. Click Merge and wait (you can check the status in the Total Channels bar).
7. Save the merged file.


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Clipboard

All of the clipboard commands involve copying data from AcqKnowledge to the standard Windows clipboard,
where the contents of the clipboard are made available for other applications. Transferring data through the
clipboard allows you to copy data from AcqKnowledge to other applications even after you have closed the
graph window and/or quit AcqKnowledge.
Data can be copied to the clipboard in two formats:
Text/Alphanumeric Copy Measurement and Copy Wave Data save information to
the clipboard in text/numeric format.
Graphic format Copy Graph transfers the image in the window to the clipboard.
Copy Measurements
Copies the contents of all visible measurement popup menus, along with the values associated with
these windows. By default, three windows are displayed (on most monitors); you can change this by
increasing or decreasing the width of the window. Once the measurements have been copied, they can
be pasted into any application that allows paste functions, including word processors, drawing
packages, and page layout programs. A sample of measurements pasted from AcqKnowledge into a
word processor follows:
BPM = 85.714 BPM delta T = 0.700 sec p-p = 0.8170 Volts
Copy Wave Data
Copies the data (in numeric form) for all channels from the AcqKnowledge graph into the clipboard.
When an area is selected, only the data in the highlighted area will be copied to the clipboard. As with
the copy measurement command, once the data is stored in the clipboard, it can be pasted into virtually
any application.
When multiple channels of data are copied to the clipboard, the data is stored in columns and rows, with
data from each channel stored in a separate column. For a four-channel record, four columns of data
will be copied to the clipboard. As with a text file, AcqKnowledge will insert a delimiter between each
column of data. The default delimiter is a tab; you can change the delimiter to either a space or tab in
the options dialog in the File > Save as dialog. See page 237 for more detailed instructions on how to
set the column delimiter. Transferring data through the clipboard performs essentially the same function
as saving data as a text file (using the File > Save As command), with the obvious exception that
transferring data through the clipboard does not save data to disk.
Note Using Copy Wave Data on larger files may crash the application due to the excessive number of
text lines generated (the problem is not the data size). For instance, one large file sample was
300,002 linesa 3 MB text file.
Copy graph
Copies the graph window as it appears on the screen to the clipboard, where it is stored in graphic
format. You can then place the graphic into a number of different types of documents, including word
processors, drawing programs, and page layout programs. The JPEG graphic format are common to
almost all applications, and images saved in these formats can be edited in most graphics packages and
many word processors.
Using the copy graph function is similar to saving a graph window as a JPEG (using the File > Save As
command), except that using the file save command writes a file to disk, whereas transferring data
through the clipboard does not save a file.

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Part C Analysis Functions 261
Copy Acquisition Settings
Creates a textual summary of the current acquisition settings and sends it to the clipboard, where it can
be pasted into the journal via Edit > Journal > Paste Acquisition settings, or pasted to another program.
The summary includes sampling rates, channel configuration, calculation channel settings, triggering
options, averaging options, and if any stimulator is active. This is useful for retaining records for
acquisition parameters (and for technical support, if necessary). Use this feature to keep a textual record
or printout of the configuration of your MP unit along with your data.
Copy Data Modification History
Copies the transformation history for all channels or a selected channel to the clipboard. Modification
history includes the transformation name, channel (analog, calculation, or digital), date & time, and
relevant transformation parameters, including starting and ending sample position.
Use Edit > Paste to move it from the clipboard to an active Journal window or other word processing
application.

Copy Focus Area Summary
Copies the starting and ending position of the focus area in horizontal axis units. Summary includes focus
area label.
Journal

The Edit > Journal sub-menu options are similar to those found in the Edit > Clipboard menu. The key
difference is that data (whether measurements or raw data) is pasted directly into the journal rather than copied
to the clipboard.
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Paste Measurements
Choosing Paste Measurements from the Edit > Journal menu will cause all visible measurement
windows to be pasted into the journal. Each time this is selected, the measurements and values are
pasted into the journal using the precision specified in the Display > Preferences dialog. You can also
change the total number of measurements displayed by adding more rows of measurements. Use the
Preferences menu (see page 419) to change the number of measurement rows or the measurement
precision displayed on the screen.
Paste Measurement shortcuts:
Keyboard: Ctrl + M
Mouse: Right-click in the Journal and choose Paste Measurement
Paste Wave Data
Converts the selected area of the waveform to numeric format and paste it into the journal in standard
text file format. As with the copy wave data command (in the Edit > Clipboard submenu) this will paste
the selected area from all channels, not just the selected channel, and will place a delimiter between the
columns when two or more channels are being pasted to the journal. By default, tab characters are used
to separate columns; you can change to comma or space delimiters in the File > Save As > Options
dialog. See the Save As section on page 244 for more information on how to change the column
delimiter.
Note Using Paste Wave Data on larger files may crash the application due to the excessive number of
text lines generated (the problem is not the data size). For instance, one large file sample was
300,002 linesa 3 MB text file.
Paste Acquisition Settings
Pastes the acquisition settings to the journal as they were copied via Edit > Clipboard > Copy
Acquisition settings.
Paste Modification History
Use after Copy Data Modification History to paste the transformation history from the clipboard for
all channels or for the selected channel to an active Journal window or other word processing
application. Modification history includes the transformation name, channel (analog, calc, or digital),
date & time, and relevant transformation parameters, including starting and ending sample position.

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Part C Analysis Functions 263
Paste Focus Area Summary
Pastes the focus area summary to the journal as copied via Edit > Clipboard > Copy Focus Area
Summary.
Show Journal
Toggle to display/hide the Journal window.
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Chapter 15 Transform menu commands
Overview

The Transform menu contains operations that primarily modify the data in the graph.
AcqKnowledge provides a number of options for post-acquisition analysis and transformations. These
transformations allow you to perform a range of operations on your data, from digital filtering and Fourier
analysis to math functions. All of these options can be found under the Transform menu, and are disabled while
an acquisition is in progress. Unless otherwise noted, all of the transformations described here apply to the
selected channel only. Some options (such as the expression and math functions) allow you to specify a channel
(or channels) to be transformed.
It is important to remember that AcqKnowledge is always selecting at least one point, and the cursor will flash
whenever only one point is selected. Some of the transformation functions (e.g., math function, waveform math)
can operate on a single sample point, and will transform a single sample point when only one is selected.
There are two ways to apply a transformation to an entire waveform.
a) For transformations that generate a dialog, check
the transform entire waveform box (usually
located toward the bottom of each dialog). This
will transform the entire waveform, regardless of
whether a single point, area, or the entire
waveform is selected.
b) For transformations that do not generate a dialog, use the Edit > Select all command prior to selecting the
transformation. This will transform the entire waveform for all of the transformation functions.
- Edit > Select All is not necessary when only a single point is selected prior to selecting the
transformation because AcqKnowledge will automatically apply the transformation to the entire
waveform since it is not possible to perform these transformations on a single point.

Note Transformations require AcqKnowledge to allocate additional memory and then load the data into
memory; when transformations are executed on large data files, the application may crash.
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Part C Analysis Functions 265
Recently Used Transformations
The Transform > Recently Used submenu allows quick access to a users most recently used transformations
and analysis commands. The Recently Used submenu also appears at the top of the Transform submenu
available from the context menus of waveforms.
The submenu lists a default of five of the most recently used transformations, with the most recently executed at
the top of the menu. To adjust the number of recent transformations displayed, select Display > Preferences.

The recently used transformation listing is saved and restored across subsequent launches of AcqKnowledge. It
also is application wide: Executing a transformation in any graph will add that transformation onto the recently
used list. The recently used list is independent for each user account.

The recently used transformations can also be launched by the keystroke combinations appearing in the menu.
(AcqKnowledge 4.2 and higher)
Digital Filters

FIR filters are linear phase filters, which mean that there is no phase distortion between the original signal and
filtered waveforms.
IIR filters are not phase linear filters, but are much more efficient than FIR filters in processing data. The IIR
filters are useful for approximating the results of standard biquadric filters of the form:
(as
2
+ bs + c) / (xs
2
+ ys + z)
These types of filters are commonly implemented in electronic analog circuitry. IIR filters are also used for
online filtering (discussed on page 134).
See Appendix B for more information about the differences between these types of filters.
Adaptive filtering is a signal processing technique that processes two different signals in relation to one another;
see page 271 for details.
To understand how digital filters work, it is important to understand the nature of analog signals and their
frequency components. All analog signals are comprised of signals of various frequencies. A commonly used
analogy is that of the color spectra. Just as white light is made up of a variety of colors that have different
wavelengths (frequencies), physiological signals are comprised of specific signals with unique frequency
signatures.
For example, an electroencephalogram (EEG) recording is comprised of several different types of signals, each
of which has a different frequency signature. Alpha waves (one of the most studied EEG signals) have a
frequency range of about 8 Hz to 13 Hz. This means that alpha waves go through a complete cycle (from peak
to peak or trough to trough) anywhere from eight to 13 times a second.
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There are, of course, signals that have other frequency signatures in EEG data. Most types of physiological data
have a number of different frequency signatures present in the overall signal. In addition, frequency components
besides the signal(s) of interest are often present. In the U.S., it is not uncommon for 60 Hz electrical noise to be
acquired along with physiological signals (in other countries, AC interference is present at either 60 Hz or 50
Hz).
Use digital filtering to retain only the frequency components of interest and remove other data (whether it is
noise or merely physiological signals outside the range of interest).
It is important to note that the way in which data is filtered depends in large part on the sampling rate at which
the original data was acquired. For instance, if data was collected at 50 samples per second (50 Hz), it is not
possible to filter out 60 Hz signals.
In fact, data must be sampled at a rate equal to at least twice the frequency of the signal to be removed. So, if
data is to be collected and the information between 80 Hz and 120 Hz is to be removed, the data must be
sampled at 120 Hz*2, or 240 samples per second (or faster). Also, each channel of data is filtered separately, so
removing one type of data from one channel will not affect any other channels.
Digital filters can be divided into four general classes:
low pass band pass high pass band stop
Descriptions of these four classes of filters follow, with visual examples of how these filters work. In each of
the four examples, a single channel of data containing frequency components in three ranges (low frequency,
mid-range, and high frequency) is acquired.
Low frequency data, by definition, has slowly changing values, much like respiration patterns or core
temperature variations.
High frequency data, compared to low frequency data, is noticeably more spiked, much like an EMG
signal. As you can tell, the high frequency wave repeats itself about five times in the time it takes the
low frequency wave to repeat once.
Mid-range data falls somewhere in between these two extremes.
In the examples that follow, one possible way that these data could have been collected is if respiration were
measured, but the measurement was contaminated with high-frequency muscle movement and mid-frequency
signal coming from AC interference. The data is then passed through a filter, where some of the frequency
components are removed.
Low pass filtering
In the example below, a low pass filter attenuates the data above a given threshold, allowing only lower
frequency data to pass through the filter.
Low
Pass
Filter
Incoming data Filtered data
Low
frequency
data
Mid
frequency
data
High
frequency
data
Low
Cutoff

High pass filtering
In the example below, a high pass filter removes the low and middle range data, but allows the high frequency
data to pass through the filter.
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Part C Analysis Functions 267
Filter
Incoming data Filtered data
Low
frequency
data
Mid
frequency
data
High
frequency
data
Hipass
High
Cutoff

Whereas the low pass and high pass filters retain data either above or below a given threshold, the next two
types of filters work with a range, or band, of data.
Band pass filter
The band pass filter, allows only the data within the specified range to pass through the filter. A band pass filter
is useful when you want to retain only specific waves from an EEG record. For instance, to retain alpha waves,
you can set the filter to only pass data between 8 Hz and 13 Hz.
Band
Pass
Filter
Incoming data Filtered data
Low
frequency
data
Mid
frequency
data
High
frequency
data
Low
Cutoff
High
Cutoff

Band stop filter
The band stop filter allows data to pass above and below the specified range. This type of filter is typically
applied to remove extraneous 60 Hz or 50 Hz noise from a data record.
Band
Stop
Filter
Incoming data Filtered data
Low
frequency
data
Mid
frequency
data
High
frequency
data
Low
Cutoff
High
Cutoff

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FIR Filters

Digital filter dialog
When you select an FIR filter type, the corresponding Digital Filter dialog will pop up, allowing you to specify
a number of different filtering options.
1. Window. The Window popup menu allows you to choose from a
variety of filtering algorithms. The filter default is set to a Blackman
type. These different Windows (described in detail in Appendix D)
allow you to fine tune the filter response.
2. Cutoff Frequency (Hz) (or threshold). Enter a fixed value or set to a
fraction of the sampling rate or to line frequency.
Sampling ratefrequency is set to a fraction of the sampling rate and
automatically updates when the sample rate is modified.
Line frequencyfrequency is set to the line frequency at which the
data was recorded.
Fixed at Fixed value guidelines are as follows:
- Low Pass Filterdata with frequency components below the
cutoff will pass through the filter, whereas frequency components
above the threshold will be removed. For low pass filters, the
default cutoff frequency is the waveform sampling rate divided by
eight and can be set to any value between 0.000001Hz and 0.5
times the sampling rate.
- High Pass Filterdata with frequency components above the
cutoff will pass through the filter, whereas frequency components
below the threshold will be removed. For high pass filters, the
default threshold is the waveform sampling rate divided by four
and can be set to any value between 0.000001Hz and 0.5 times the
sampling rate.
- Band-type Filtersa low threshold and a high threshold must be specified to define the band of data
(the frequency range) that is either passed or stopped, depending on whether it is a Band Pass or Band
Stop filter. In either case, the default for the low threshold is the waveform sampling rate divided by
eight and the default for the high threshold is the waveform sampling rate divided by four. The
threshold settings can take on any value from 0.000001Hz and 0.5 times the sampling rate, but the two
thresholds cannot be set to the same value and the high threshold must be greater than the low
threshold.
3. Number of Coefficients. Enter a fixed value or enable the optimize option.
- Fixed atThis determines how well the filter will match the desired cutoff frequency (or range). The
minimum number of coefficients is 3 and the maximum must be less than the total number of sample
points in the selected area. The software will truncate the maximum number of coefficients to the
highest odd number less than the total.
- Optimize for sample rate and cutoffthe number of coefficients is set as four times the sampling rate
divided by the cutoff frequency of the filter. Optimize does not necessarily produce the best quality
filter, but it takes less time.
The recommended number of coefficients is
4 x (waveform sampling rate/lowest frequency cutoff for the filter)
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Part C Analysis Functions 269
For every filter except the band pass, the lowest frequency cutoff is equal to the specified cutoff frequency
for the filter; for the band pass filter, the lowest frequency cutoff is the low frequency cutoff setting. Filters
that use a small number of coefficients tend to be less accurate than filters that use a large number of
coefficients. Larger coefficients increase filter accuracy, but also increase the processing time required to
filter the data.
To see how changing the number of coefficients affects the way data is filtered, it can be useful to examine
the filter response patterns. In the example below, data was collected at 500 Hz and the band stop filter was
designed to remove 60 Hz noise using a low cutoff of 55Hz and a high cutoff of 65Hz. The same data was
band stop filtered using 39 coefficients (upper waveform) and then 250 coefficients (lower waveform).

Along the horizontal axis, the units are scaled in terms of frequency, with lower frequencies at the left of the
screen. The values along the vertical axis are scaled in terms of dB/V and indicate the extent to which
various frequencies have been attenuated.
In both filter response waveforms, there is a downward-pointing spike that is centered on 60 Hz. The
baseline of the filter response corresponds to a value of approximately 0 on the vertical axis, indicating that
the signals significantly above or below 60 Hz were not attenuated to any measurable extent. As you can
tell, however, the filter does not chop the data at either 55Hz or 65Hz, but gradually attenuates the data as
it approaches 60 Hz.
For example, the upper waveform in the filter response plot represents data that was filtered using a value of
39 coefficients. The slope is relatively shallow when compared to the lower waveform, which represents a
filter response performed with 250 coefficients. Although the filter that used 250 coefficients took slightly
longer to transform the data, the filter response pattern indicates that the data around 60 Hz is attenuated to
a greater degree. Also, the 250-coefficient filter started to attenuate data considerably closer to the 55 Hz
and 65 Hz cutoffs, whereas the default filter began to attenuate data below 55 Hz and above 65 Hz.
TIP: A good rule of thumb is to use a number of coefficients greater than or equal
to two times the sampling rate divided by the lowest cutoff frequency
specified. For example, if running a low pass filter at 1 Hz on data sampled at
100 Hz, choose at least (2 x 100/1) or 200 coefficients in the filter. Additional
coefficients will improve the response.
4. Show Filter Response. When checked, this option generates a plot of the
filter response in a new window, labeled Frequency Response (see
example above).
Units: Select linear units or dBV.
5. Dont modify waveform. This option is useful in conjunction with the Show Filter Response option.
When both boxes are checked, AcqKnowledge will produce a plot showing the filter response, but will not
modify the waveform. This allows you to repeatedly specify different filter options (without modifying the
waveform) until the desired frequency response is achieved.
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6. Filter entire wave. If this option is checked, AcqKnowledge will filter the entire wave and replace the
original. If you want to keep the original, duplicate it prior to filtering.
IIR Filters
To access the IIR filter dialog, click the Transform menu, scroll to select Digital Filters, drag right to IIR and
drag right again for the filter options. For all filter types, the software will limit the frequency setting so it
cannot exceed one-half the channel sampling rate. For real-time filter options, see page 134.

Low Pass and High pass Pass data that falls below or above the specified standard. The Low Pass default is
waveform sample rate/8; the High pass default is waveform sample rate/4.
Band Pass (low + high) Pass a variable range of data. Specify a low frequency cutoff and a high frequency
cutoff to define the range or band of data that will pass through the filter;
frequencies outside this range are attenuated. For the Band Pass Low + High filter,
the low default is waveform sample rate/8 and the high default is waveform sample
rate/4.
This filter is best suited for applications where a fairly broad range of data is to
be passed through the filter. For example, apply to EEG data to retain only
alpha wave activity.
Band Pass (single freq) Requires only a single frequency setting, which specifies the center frequency of
the band to be passed through the filter. The width of the band is determined by
the Q setting of the filter (discussed in detail below). Larger Q values result in
narrower bandwidths, whereas smaller Q values are associated with a wider band
of data that will be passed through the filter. This filter has a bandwidth equal to
Fo/Q, so the bandwidth of this filter centered on 50 Hz (with the default Q=5)
would be 10 Hz. Although functionally equivalent to the Band Pass (low + high)
filter, this filter is most effective when passing a single frequency or narrow band
of data, and to attenuate data around this center frequency. The Band Pass (single
frequency) default is waveform sample rate/8.
Band Stop (single freq) Defines a range (or band) of data and attenuates data within that band (the opposite
function of a band pass). This filter is implemented in much the same way as the
standard Band Pass, whereby a center frequency is defined and the Q value
determines the width of the band of frequencies that will be attenuated. The Band
Stop (single frequency) default is waveform sample rate/8.
Q coefficient The online filters are implemented as IIR (Infinite Impulse Response) filters, which
have a variable Q coefficient. The Q value entered in the filter setup box
determines, in part, the frequency response of the filter. This value ranges from
zero to infinity, and the optimal (critically damped) value is 0.707 for the Low
Pass, High pass and Band Pass filters. A Q of .707 for any of these filters will
result in a second order Butterworth response. The Q is set to a default of 5.000 for
the single frequency Band Pass and Band stop filters. For more details about the Q
setting, see the Appendix.
Sampling rate Sets the Frequency to a fraction of the sampling rate and automatically updates when the
sample rate is modified.
Line frequency Sets the Frequency to the line frequency at which the data was recorded.
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Part C Analysis Functions 271
Adaptive Filtering


C See the Adaptive Filtering Calculation
Channel on page 149.
Adaptive filtering is a signal processing technique that
processes two different signals in relation to one another
and can be used for noise estimation, noise reduction,
general-purpose filtering, and signal separation. Adaptive
filtering creates efficient high-quality filters with a minimal
number of terms, which can be very useful in blocking
mains interferences or other known periodic disturbances.
Useful for noise filtering where it is possible to acquire
a signal that is correlated to the noise (similar to the
way noise-cancelling headphones detect and remove
outside noise). Applications include removing EMG
from ECG or EOG from EEG.
The weights within an adaptive filter are modified on a step-by-step basis. AcqKnowledge uses the N-tap FIR
adaptive filter, with coefficients updated using least means squares (gradient) feedback.
Source signal
The source channel will be replaced by the adaptive filter results.
Noise signal
The noise channel is the signal that is correlated with the noise to be eliminated from the Source; it is
not modified by adaptive filtering.
Source and Noise channels must have the same sampling rate.
Order
Specify a positive integer for the number of terms to be used in the internal FIR filter.
Step size
Provides mu, the rate of adaptation of the coefficients within the FIR filter.

Comb Band Stop Filter
Comb Band Stop filters out a fundamental frequency and its overharmonics (integer multiples of the base).
Resonance, aliasing, and other effects may generate interference at multiples of a base frequency. The Comb
Band Stop filter combines all the required filters instead of requiring a separate filter for each interfering
overharmonic.

Transformation Dialog Calculation Channel Dialog
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Resonance, aliasing, and other effects may generate interference at multiples of a base frequency. The Comb
Band Stop filter combines all the required filters instead of requiring a separate filter for each interfering
overharmonic. Comb Band Stop filters remove a fundamental frequency and its overharmonics (e.g., integer
multiples of the base frequency) from a signal, and are useful for removing noise. AcqKnowledge approximates
a Comb Band Stop filter by cascading a series of IIR Band Stop filters, and is limited to removing frequencies
and overharmonics. The number of filters used can be fixed at a particular number (e.g., limiting the number of
harmonics to filter out) or configured to automatically remove all possible harmonics for any given sampling
rate.
- Mac OS Use the "Comb Band Stop Filter" Automator action to integrate Comb Band Stop
filters into Workflows.
For a given base frequency and quality factor Q, the comb filter approximation will be given by the set of
following formulas:
( )( ) x F F F F y
ke e e e
=
3 2

where F represents a standard two-tap IIR band stop filter for the frequency with coefficients
computed using the quality factor Q.
The number of overharmonics of the base frequency to be removed is given by the integer value k. The
maximum allowable number of overharmonics may be automatically determined given the sampling
frequency f
s
:
(
(

=
e 2
max
f
k
s

This limits the maximum overharmonic frequency to be less than the Nyquist of the sampling
frequency.
After the first comb filter is performed, the most recently used settings for the comb filter will be displayed,
(except for Transform entire wave, which will be reset each time the dialog is opened).
Textual export will include the source channel, base frequency, quality factor, and number of harmonics.
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Part C Analysis Functions 273

Comb Band Stop Filter Dialog
number of samples Width of the selection.
@ samples/sec Waveform sampling rate of the source channel.
- The channel sampling rate of the calculation channel can not exceed the channel sampling
rate of the source channel. Downsampling will be applied to the source channel prior to
comb filter processing, if required, and all Nyquist frequency restrictions will be determined
from the calculation channel sampling rate.
Frequency FixedThe comb filter will remove this base frequency and integer multiples of this frequency.
- Must be positive and less than the Nyquist frequency (half the sampling rate).
Sampling rateSets the frequency to a fraction of the sampling rate and automatically updates
when the sample rate is modified.
Line frequencyUses the line frequency at which the data was recorded.
Q Quality factor used when computing the coefficients of the IIR notch filters.
- Must be positive.
all up to Nyquist Removes all integer multiples of the base frequency. This will include all multiples of the base
frequency that are less than the Nyquist frequency.
Harmonics Removes the base frequency and integer multiples of the base frequency up to and including the
multiple contained in the edit field
- Must be an integer greater than 0 and must not exceed k max
- The final multiple must be less than the Nyquist frequency. If it is not, the input will need to
be corrected before the comb filter can be applied.
OK If the settings are valid, executes the comb filter transformation. Verification of certain calculation
channel parameters does not occur until the start of acquisition as sampling rates may be changed
after calculation channels are configured.
Prior to the start of acquisition, the following will be checked:
- source channel to ensure it is still being acquired.
- base frequency of the comb filter to ensure it is less than the Nyquist frequency of the
channel sampling rate.
- if the user has manually specified that a fixed number of overharmonics should be used, the
number of overharmonics to ensure the highest used overharmonic does not exceed the
Nyquist frequency of the channel sampling rate.
If any of the parameters are invalid, a prompt will be displayed indicating which settings are
incorrect and must be fixed for the acquisition to be started.
Cancel Quits without modifying any data.
Source All enabled analog, digital, and lower-index calculation channels.
Label When the calculation type of a channel is changed to comb filter, the title of the channel will be
replaced with the default label Cn Filter where n is the index of the calculation channel.
- Must be 40 characters or less.
Preset Displays the title of any Calculation Preset currently applied to the calculation channel.
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Fourier Linear Combiners
Transform > Fourier Linear Combiners:


C See FLC Calculation Channel
options on page 148.
C See FLC references on page 275.
Fourier Linear Combiners are linear combinations of
adaptable sinusoidal functions that are particularly well
suited to processing cyclic data. Sine and cosine harmonics
of a base frequency are summed together and the order is
the fixed number of harmonics used in the model. Step size
provides mu, the gain factor used to adjust the weights of
the harmonics at each processing step. Step sizes must be
much less than 1 for the system to converge. As step sizes
decrease, relaxation time lengthens. The FLC model is
adjusted based on the source data using least means square
(LMS) feedback and the bias compensates for DC offset.

Basic FLC
Simple summation of fixed numbers of sines and cosines; uses
harmonics of a fixed frequency and adjusts weighting coefficients
of the mixture.
Operates on a single channel at a time.
Well suited for extracting data of a known frequency band from a
signal with a stable frequency.
Use as an adaptive noise filter to remove non-periodic and
semi-periodic noise uncorrelated to the base harmonic
frequency.

Scaled FLC
Fundamental harmonic frequency can vary on a cycle-to-cycle
basis. The frequency remains fixed within a single cycle and must
be known before processing.
Scales the harmonics used in each cycle based on cycle
boundary events (defined through the Cycle Detector, ECG
Analysis, or manually). Events from one signal can be used to
drive analysis of another signal.
Well suited for signals with detectable boundaries, such as ECG.
Use to extract information that is tightly coupled to other
cyclic signals, such as extracting ICG based upon
Knowledge of the RR cycles of the ECG.

Weighted-Frequency FLC
Base frequency of the harmonics is variable; adapts the
frequency in response to the input signal using LMS feedback;
the frequencies are similarly adjusted to the amplitudes.
Operates on a single channel at a time.
Well suited for modeling periodic signals of an unknown and
potentially varying frequency and/or amplitude.
No cycle boundaries or frequencies need to be pre-
determined.
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Part C Analysis Functions 275
Coupled WFLC/FLC
Runs a WFLC on the signal to determine the harmonic frequency and
then runs the result through an FLC using the computed harmonic.
The second FLC can be run on the same or a different channel.
The transformation will occur in the channel designated as Output.
Well suited for real-time extraction of information from one signal
based upon the frequencies contained in another signal.
Use to remove movement noise from ECG.
Unique configurations can be established with two input signals,
one for frequency and one for amplitude.

FLC References
The basic Fourier linear combiner (FLC) is described by Vaz and Thakor.
C Christopher A. Vaz, and Nitish V. Thakor, Adaptive Fourier Estimation of Time-Varying Evoked Potentials,
IEEE Trans. Biomed. Eng., VolBME-36, pp. 448-455.
The weighted-frequency Fourier linear combiner (WFLC) and the coupled weighted-frequency Fourier linear combiner
(CWFLC) are described by Riviere, Rader, and Thakor.
C Cameron N. Riviere, R. Scott Rader, and Nitish V. Thakor, Adaptive Canceling of Physiological Tremor for
Improved Precision in Microsurgery, IEEE Trans. Biomed. Eng., Vol BME-45, pp. 839-846.
The scaled Fourier Linear Combiner (SFLC) is described by Barros, Yoshizawa, and Yasuda.
C Allan Kardec Barros, Makoto Yoshizawa, and Yoshifumi Yasuda, Filtering Noncorrelated Noise in
Impedance Cardiography, IEEE Trans. Biomed. Eng., Vol BME-42, pp. 324-327.


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Math Functions
AcqKnowledge allows you to perform a wide range of mathematical and
computational transformations after an acquisition has been completed. Unless
otherwise noted, each of these functions applies only to the selected area of the
selected channel. If no area is selected (i.e., a single data point is selected), the
cursor will blink and AcqKnowledge will transform the entire wave. If a math
function attempts to divide by zero, a zero will be returned.
For complex transformations involving multiple functions, you may want to use
the Expression transformation (see page 292 for details).
The following table describes the commands available in the Transform > Math functions menu:
Transform > Math Explanation of Command
Abs (Absolute Value) Computes the absolute value of the data. All negative data values are made
positive, with no change in magnitude. This function can be used to rectify data.
Atan (Arc Tangent) Returns the arc tangent of each data point in radians. This rescales the data such
that the range is from -t/2 to t/2.
Connect endpoints
(Connect the endpoints)
Draws a line from the first selected sample point to the last selected sample point
and interpolates the values on this line to replace the original data. The connect
endpoints function is very useful for removing artifacts in the data or in generating
waveforms.
In the example below, the noise spike in the data is an undesired measurement
artifact that should be removed. You could cut the section of data, but then all
subsequent data points would shift left. In order to preserve the time series of the
data, you could use the connect endpoints command to draw a straight line
(although not necessarily flat) that connects the two extreme sample points of the
selected area.


Area selected before (top) and after (bottom) connect endpoints function

Exp (Exponential)
Computes the function e
x
, where x is the waveform data and e is 2.718281828.
This is the base of the natural logarithms.
Limit (Limit data values) Clips data outside the range specified by the set of thresholds in the limit dialog.
This function will prompt you for an upper and lower limit. Any data values outside
these limits will be clipped at the closer limit. Although both a high and low
threshold must be entered, To limit only one extreme (high or low) while leaving
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Part C Analysis Functions 277
Transform > Math Explanation of Command
the other extreme unaffected. For instance, if you wanted to limit data so that all
negative values were set to zero but the positive values were left unchanged, you
would set the low threshold to zero and the high threshold to 99 (or some other
large positive value that exceeds the maximum value for that channel).
Ln (Natural Logarithm) Computes the natural logarithm of the selected section. The inverse of this function
is the exponential function, Exp.
Log (Base 10 Logarithm) Computes the base 10 logarithm of the selected section.
In order to perform the inverse of this function, which would be 10
x
, use the
Waveform Math power operator with the constant k=10 as the first operand and
the waveform data as the second operand.
Noise Converts the selected section into random data values between 1.0 and +1.0.
This is mainly useful for creating stimulus signals and other waveforms.
Sin (Sine) Calculates the sine of the selected section. The data is assumed to be in radians.
Sqrt (Square Root) Takes the square root (\) of each data point in the selected section.
Threshold (Threshold
data values).
Transforms all data points above the threshold to +1 units, and converts all values
below the lower threshold to 0 units. Once the data crosses a threshold it will
continue to be set to +1 for the upper cutoff and 0 for the lower cutoff, until it
crosses the opposite threshold. The most common application of this function is to
serve as a simple peak detector, the results of which can be used in rate or phase
calculations.
Threshold Algorithm
Assume a domain variable

t e t
start
, t
start
+1, t
start
+ 2, { } with t
start
being an
integer, a real-valued signal y(t) defined for all t, and two real valued levels y
low
and
y
max
satisfying the relation y
low
s y
high
.
Define the threshold function thresh(t) function such that:
thresh(t
start
) =
1 y(t
start
) > y
low
0 y(t
start
) < y
low




thresh(t) =
0 y(t) < y
low
1 y(t) > y
high
thresh(t 1) y
low
s y(t) s y
high






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Template Functions

The Template Functions are useful for comparing waveforms. Technically, the template functions provide
correlation, convolution and mean square error transformations of a template waveform against another
waveform. To activate the full template menu, select an area and then select set template.
NOTE: To determine a level of comparison between two waveforms, use the
Correlation function.
All the template functions perform a mathematical operation of the template waveform on the waveform to be
compared, move one sample forward, and repeat the multiplication until the end of the longer waveform is
reached.

Set Template
Use the following ECG waveform as an example. An abnormality exists in the record. After detecting an
abnormality, you should find out if there are other (similar) abnormalities in the record. To do that, you need to
select the pattern youd like to search for, and then compare that pattern to other data sets in the file.
Selecting a section of a wave to be used as a template:
1) Highlight the section to be used as a pattern.

2) Click the Transform menu and choose Set template from the Template functions submenu. This copies
the selected portion into a buffer for subsequent template functions
3) Select the waveform and position the cursor at the beginning of the data.
4) Choose Correlation from the Template functions submenu. The center waveform in the graph below
shows the result of the correlation.
Note the higher amplitude peaks where the template data more closely matches the waveform. The lower
waveform illustrates the mean square error function, which is similar to the correlation function.
This indicates that there are two abnormal beats in the record. The first one appears at about 3 seconds and
is the one used as a template; the second one appears at about 11 seconds.
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Part C Analysis Functions 279

Result of correlation and mean square error functions
5) Use the zoom tool to inspect the abnormalities more closely.

Remove mean
A drifting baseline can be a problem in comparing waveforms. If you perform a Template function and the
template or the waveform has a slowly moving baseline, you can increase the effectiveness of the comparison
by choosing Remove mean from the submenu of the Template function. The remove mean option causes the
mean amplitude value of the template and the compared section of the waveform to be subtracted from each
other before the sections are compared. This way, a large baseline offset will have very little effect on the
comparison. This option is toggled every time it is selected and is enabled when a check mark is present.
For example, the following graph shows the original waveform at the top, the correlated waveform with mean
removal in the middle, and the same correlation without mean removal at the bottom. Note how the mean
removal effectively compensates for the drifting baseline in the original waveform.

Correlation with and without mean removal
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Template algorithms
The template functions are: correlation, convolution, mean square error, inverse mean square error, normalize
cross correlation and adaptive template matching.
a) Correlation is a simple multiplication and sum operation (as shown in the preceding example). The template
is first positioned at the cursor position in the waveform to be correlated. Each point in the template
waveform is multiplied by the corresponding point in the data waveform (the waveform to be correlated)
and summed to produce the resulting data point. The template is then moved one data sample forward and
the operation is repeated to produce the next resulting data point. The resulting data points replace the
waveform to be correlated.
The correlation function algorithm can be expressed by the following formula, where f
output
(n) is the
resulting data point, f
template
(k) is the template waveform data points, and K is the number of data points
in the template:

K
1 = k
waveform template output (n) f * (k) f = (n) f


b) Convolution is identical to the correlation function except that the template waveform is reversed during the
operation. This function is not generally useful by itself, but can be used as a building block for more
sophisticated transformations. The convolution function algorithm can be expressed by the following
formula, where f
output
(n) is the resulting data point, f
template
(k) is the template waveform data points, and
N is the number of data points in the template:
f (n) = f (-k) * f (n + k) output template waveform
k = -N/ 2
N/ 2 - 1


c) Mean square error positions the template at the cursor position in the waveform to be compared. Each point
in the template waveform is subtracted from the corresponding point in the waveform to be compared. The
result is squared and summed to produce the resulting data point. The template is then moved one data
sample forward and the operation is repeated to produce the next resulting data point. The resulting data
points replace the waveform.
The mean square error function tends to amplify the error (or difference) between the template and the
waveform, which makes it useful when you are looking for an extremely close match rather than a general
comparison. When a match is found, the mean square error algorithm returns a value close to zero.
The mean square error function algorithm can be expressed by the following formula, where f
output
(n) is
the resulting data point, f
template
(k) is the template waveform data points, and K is the number of data
points in the template:
f (n) = [f (k) - f (n)] output template waveform
k = 1
K

2


d) Inverse Mean square error simply inverts the result of the mean square error algorithm. Accordingly, when
this algorithm finds a match between the template and the data, the algorithm returns the inverse of a value
close to zero and, typically, a large positive spike will occur at the point of the match.

e) Remove Projection Template removes the projection of a reference signal from another part of a signal
(whereas the other template functions revolve around the comparison of a portion of a signal against a
reference signal).
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Part C Analysis Functions 281
Remove Projection treats the template in memory as a vector. The projection of the selected area onto the
template is computed as a vector dot product. This projection is then removed from the source data. After a
remove projection transformation, the remaining data consists of the part of the signal that is the most
unrelated to the template.
Remove Projection can be useful for emphasizing signal differences. For example, it may be useful for
exploring differences in an arrhythmia in comparison to a normal reference beat. It may also be useful as a
denoising building block by removing the projection of a signal against idealized noise in the template.
The number of samples in the template should match the number of samples in the selected area of source
data.
- Dot product is undefined for vectors of mismatched dimensions.
- If the template is longer than the selected source data, the template will be shortened (for that single
transformation; it will be restored afterward) so its length matches the selection width.
- If the selection is longer than the template, any data occurring after the end of the template will not
be transformed.
To create a Remove Projection template:
1. Highlight the portion of data to be used as the reference signal.
2. Transform > Template > Set Template.
3. Highlight the portion of the data to be analyzed.
4. Transform > Template > Remove Projection.

f) Normalized cross-correlation is useful when searching for variations in the signal. Regular cross-correlation
(Transform > Template > Correlation) can exhibit large amplitude spikes when the energy of a signal varies
greatly or amplitudes change suddenly, causing jumps that are not necessarily indicative of a match with the
template. Normalized cross-correlation is a statistical method that can help resolve these issues by applying
normalization to both the template and signal being searched. This reduces the effect of amplitude variation
in the result, making normalized cross-correlation useful for template matching purposes.
This transformation computes the windowed normalized cross-correlation, and results in a value between -1
to 1, which indicates the linear fit of the data set. Normalized cross correlation is defined as:

= =
=


=
L
i
L
i
i i
L
i
i i
y y x x
y y x x
0 0
2 2
0
) ( ) (
) )( (


where x = template
y = signal
L = length
= mean value of the signal f
At the end of the transformation, the source data will be replaced with the sliding NCC values. Data outside
the selected area will be left unmodified. If the selected area is zero width when the transformation is to be
executed, the entire waveform will be transformed.
If selection is shorter than the template, the missing data at the right end of the selected area will be filled
with zero padding until it matches the length of the template. This padding occurs in memory and will not
affect the source data in the graph. The same zero padding is used when computing NCC at the end of every
selected area when the template is running off the end of the data. This zero padding should trend the NCC
to zero at the right edge of the transformed area, in most cases.
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Adaptive Template Matching
Many different types of physiological analysis involve
locating repetitive features within a signal. These may
occur at regular intervals or may occur sporadically.
Sometimes the features of interest may be intermingled
with other results, such as occasional heartbeat
arrhythmias occurring in a long-term ECG recording.
Template matching is one frequently used approach for
locating areas of waveforms that exhibit certain
characteristics. An example feature is specified as the
input template and then, using cross correlation or related
methods, the areas of an arbitrary wave that most strongly
match the example can be located.
Adaptive Template Matching allows the template to vary
during execution to incorporate changes to the
morphology of signal features. The adaptation consists of
a moving average of a number of the most recent
matching features. A template match will be defined as a
peak in the windowed normalized cross correlation of the
adapting template with the signal.
Normalized cross correlation helps to eliminate artifact due to baseline shift and changes in overall power
and amplitude. This heuristic is sensitive to waveform morphology instead of amplitude.
Template width
The number of samples in the template that will be used as the initial template for the transformation, as
set using Transform > Template Functions > Set Template.
Note One template is shared globally by all graphs and data views in AcqKnowledge.
Average template window size
Input positive integers only. Provides the number of previous matches to be used for constructing the
average template estimate.
Correlation threshold
Floating point input in the range -1 to 1. Provides the threshold used for peak detection on the
normalized cross correlation signal. Corresponds to r in the algorithm description.
Normalize matching data before updating average template
Toggle check box. When enabled, the reference set normalization algorithm option is used. This
performs mean subtraction and unit magnitude normalization to every member of the reference set prior
to constructing the average template. This option can help to compensate for unintentional weighting of
the windowed average template towards larger amplitude data.
Reject matches closer than
When checked, the minimum match interval algorithm option is used. This rejects matches that are too
close together and can compensate for degeneration of the algorithm into continual matching due to
signal self similarity. The edit field contains the minimum width that must separate valid matches. The
width must always be a positive number. The popup menu specifies the units of the separation interval.
Its contents are dependent on the horizontal axis type:
Time (seconds & HH:MM:SS) Frequency Arbitrary
samples samples samples
milliseconds Hz arbitrary units
seconds
minutes
hours
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Part C Analysis Functions 283
Output
Show normalized cross correlation values provides access to the sequence of correlation values that is
examined by the heuristic for potential matches. Viewing the normalized cross correlation signal can
provide feedback that is useful for proper threshold selection and for detecting whether the heuristic has
fallen into one of its degenerate cases (e.g. NCC signal hovering around the threshold for extended
periods of time). When checked, a new channel will be added into the graph containing the normalized
cross-correlation values computed by the algorithm. The channel will be labeled NCC Values.
Generate synchronization waveform allows for the generation of spike trains. The value of the wave in
the graph will be zero by default. At each sample position where a match with the average template is
triggered, the wave value will be set to one. A single sample position set to 1 indicates a single valid
match. This synchronization wave can be used in conjunction with the cycle detector to perform further
data reduction, input to the rate detector for computing match frequencies, and other analysis.
Define events at match locations output allows placement of an event on the waveform being analyzed
at the location of each valid match. The event output can allow adaptive template matching to be used
to construct classifiers that provide event locations for further data reduction with the cycle detector.
TypeUsed to choose the type of event that will be defined at match locations. Displays the
standard hierarchical menu list of event types.
LabelLabel to be given to events defined at match locations.
Transform entire wave
When checked, the entire waveform will be analyzed. When unchecked, only the selected area will be
transformed.
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Integral
Integral is essentially a running summation of the
data. Each point of the integral is equal to the sum
of all the points up to that point in time, exclusive
of the endpoints, which are weighted by half. The
exact formula is below, where f( ) is the data values
and ATs is the horizontal sampling interval:
f (n) = f (k) f (n -1) + f (n)] / 2]* T output input
k = 1
n -1
input input

+[[ A s

The units will be (amplitude units horizontal units). The integral function can be used to compute the area
under the curve in a continuous fashion. For instance, if you had data acquired by an accelerometer, the integral
of the data would be the velocity, and the integral of the velocity would be the distance. As with all
transformations, this function can be applied to either a selected area or to the entire waveform.
Derivative

Derivative calculates the derivative of the selected area of a waveform. Since high frequency components return
nonsensical results in a derivative, a low pass filtering function is included in the Derivative function (see page
266 for more information on low pass filters). Derivative is based on an FIR filter implementation.
The Filter Response for a Derivative transformation will be displayed as a linear graph, not in (log). The
Derivative FIR filter frequency response will appear as a linearly increasing magnitude up to the point of the
specified cutoff frequency, at which point, the filter magnitude will drop off sharply.

Derivative can provide a more meaningful result than Difference (which often has a higher than required
frequency response, thus processing potentially undesirable data). However, if your data is already well
behaved (i.e., low pass filtered or contains little or no high frequency information), you can use Difference
with a 2-sample interval to quickly generate results very similar to Derivative.
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Part C Analysis Functions 285
Cutoff Frequency The value entered in the cutoff frequency box should be roughly equivalent to the highest
frequency component of interest present in the time series data. The default cutoff
frequency is 0.125 times the waveform sampling rate.
Sampling rateSets the frequency to a fraction of the sampling rate and automatically
updates when the sample rate is modified.
Line frequencyUses the line frequency at which the data was recorded.
# of Coefficients FixedThe default number of coefficients is (4 x waveform sampling rate)/Cutoff
Frequency. As the number of coefficients (Q) increases, the Derivative becomes more
accurate. Fixed can produce better filters but may take longer to execute.
Optimize for sample rate and cutoffEstimate the number of coefficients as four times
the sampling rate divided by the cutoff frequency of the filter. Optimize does not
necessarily produce the best quality filter, but takes less time.

Units Select linear units or dbV.


TIP: A good rule of thumb is to use a number of coefficients greater than or equal to
two times the sampling rate divided by the lowest cutoff frequency specified. For
example, if running a low pass filter at 1Hz on data sampled at 100 Hz, choose at
least (2 x 100/1) or 200 coefficients in the filter. Additional coefficients will
improve the response.
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Integrate
The Integrate transformation operates
the same as the Integrate calculation
see page 122, except it does not have a
Max Cycle option, which is not relevant
post-acquisition, and Reset via channel
with mean subtraction enabled functions
differently online and offline.

Root mean square is implemented as:
Sqrt(sum(x^2)/(n))
Reset
Online Mean subtraction causes the online version to be delayed by the mean cycle length. It waits for
that period of time to pass so it can determine a mean value for the initial cycle, and it then
tries to re-compute this mean for each cycle. If the resets are too short or too long, the window
expires and the processing halts again until a new mean can be recomputed. Online processing
may reset from threshold crossing in the control channel or window expiration when it loses
mean tracking.
Offline Since all the data is available, the mean is computed from the data in the channel and doesn't
delay the signal. Also, since it isnt doing windowed means, there are no window expiration
events that are inserted. Offline processing may reset from threshold crossing in the control
channel.
Output Reset

Enable the
checkbox
option to
create an
Event at each
signal reset.


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Part C Analysis Functions 287
The Integrate formula is the same in the calculation (online, real-time) mode and the transformation (off-line,
post-processing) mode; it varies only based on the parameters selected.
Notes
- For the first points, value of index i will be less than or equal to zero; it means that for
summation you have only values beginning with ( )
1
x f .
o For the first point for summation you have: ( )
1
x f , ( )
0
, x f ( )
1
x f .
( )
1
x f and ( )
0
x f - dont exist, so you have only ( )
1
x f .
o For the second point for summation you have: ( )
0
, x f ( )
1
x f , ( )
2
x f .
( )
0
x f - doesnt exist, so you have only ( )
1
x f + ( )
2
x f .
- The Integrate formula is implemented as a Standard Deviation formula (see
mathworld.wolffram.com > Wolfram Research > equation 5 at
http://mathworld.wolfram.com/StandardDeviation.html).
- The Root Mean Square formula is identical to the Standard Deviation formula, but without mean
removal; this is the n-1 definition.
o For an explanation of n-1 versus n in the formula, see notes as a pdf or
http://www.uic.edu/classes/mba/mba503/971/503nts3.htm.
o For a window size n, to convert from the n-1 definition to the n definition, use
n
n ) 1 (

- The formulas to calculate RMS are optimal for data with a
zero mean (typical for biopotential data). For data with a non-
zero mean, scaling can be applied. Click the Scaling button
in the Integrate dialog (or click the channels vertical scale to
generate the Vertical Scale dialog and then click the Scaling
button), and then enter the following parameters:
Input value Map (Scale) value
10 7.07107
-10 -7.07107




1. Via samples, no extra parameters selected
( ) ( ) x x f x F
j
s j i
i j
A =

+ =
*
1

Where:
i - index for source values (***the real range is 1..j);
j - index for destination values (1..n);
n - number of samples;
i
x , - values of points at horizontal axis;
j
x
( )
i
x f - values of points of a curve;
( )
j
x F - integrated values of points of a curve;
s number of samples to average across;
1
1

= A
n
x x
x
n
- horizontal sample interval;
1
, x x
n
- values at horizontal axis at the endpoints of selected area.


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Integrate formulas, continued See Notes on page 287
( ) ( ) ( ) x x f ABS x F
j
s j i
i j
A =

+ =
*
1
2. Via samples, rectify

Where:
i - index for source values (***the real range is 1..j);
j - index for destination values (1..n);
n - number of samples;
i
x
j
x , - values of points at horizontal axis;
( )
i
x f - values of points of a curve;
( )
j
x F - integrated values of points of a curve;
s - number of samples to average across;
1
1

= A
n
x x
x
n
1
, x x
n
- horizontal sample interval;
- values at horizontal axis at the endpoints of selected
area.
3. Via Samples, root mean square (RMS)
( )
( ) ( )

Where:
1
1
2

=

+ =
s
x f
x F
j
s j i
i
j
i
i
x
j
x
( )
i
x f
- index for source values (***the real range is 1..j);
j - index for destination values (1..n);
n - number of samples;
, - values of points at horizontal axis;
- values of points of a curve;
( )
j
x F - integrated values of points of a curve;
s - number of samples to average across.
4. Via samples, root mean square, remove baseline

( )
( )
( )
1
1
2
1

(
(
(
(


+ =
+ =
s
k
x f
x f
x F
j
s j i
j
s j m
m
i
j

Where:
i and m- indexes for source values (***the real range is 1..j);
j - index for destination values (1..n);
n - number of samples;
i
x , - values of points at horizontal axis;
j
x
( )
i
x f - values of points of a curve;
( )
j
x F - integrate values of points of a curve;
s - number of samples to average across.
k - coefficient: for the first few points that have index j < s k=j,
for the other points with j > =s k=s
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Part C Analysis Functions 289
Smoothing

The smoothing function is a transformation that computes the moving average of a series of data points and
replaces each value with the mean value of the moving average window. This has the same effect as a crude
low pass filter, with the advantage being that smoothing is typically faster than digital filtering.
Samples AcqKnowledge allows you to set the width of the moving average window (the number of
sample points used to compute the mean) to any value larger than three. By default, this is set
to three samples, meaning that AcqKnowledge will compute the average of three adjacent
samples and replace the value of each sample with the mean before moving on to the next
sample. For data acquired at relatively high sampling rates, you will probably want to set the
smoothing factor to a higher value, since smoothing three sample points when data is
collected at 1000 Hz will only average across three milliseconds of data, and will typically do
little to filter out noise. To set the size of the window, enter a value in the Transform >
Smoothing dialog.
This function is most effective on data with slowly changing values (e.g., respiration, heart
rate, GSR) when there is noise apparent in the data record.
Mean value Mean value smoothing is the default and should be uses when noise appears in a Gaussian
distribution around the mean of the signal. The Mean value smoothing formula is shown
below, where m is the number of points in the window and n is the sample number:
m / (k) f = (n) f
1)/2] - [m + n k
(m/2) - n = k
input output

=

Median value Use Median value smoothing if some data points appear completely aberrant and seem to be
wild flyers in the data set.
The Median value smoothing formula is shown below, where m is the number of points in
the window and n is the sample number:
[m/2]) n [m/2]; - (n median = (n) f output +
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Difference

The Difference function measures the difference (in amplitude) of two sample points separated by an arbitrary
number of intervals. The difference is then divided by the total interval between the first selected sample and
the last selected sample.
When you select the difference transformation, a difference interval dialog will be generated and you can enter
the number of intervals between samples (default of 1).
For data with no high frequency components, a 1-interval difference transformation approximates a
differentiator.
Since it is not implemented as a convolution, Difference is much faster than the derivative function.
The formula for the difference transformation is shown below, where m is the number of intervals difference,
[ ] rounds the integer down, n is the sample number, and ATs is the horizontal sampling interval:
f
output
(n) = f
input
(n + [m/2])f
input
(n[(m+1)/2])
(ATs * m)
Example for boundary values when
m = 3:
f
output
(0) = (f
input
(1)f
input
(0)) / (ATs * m)
f
output
(1) = (f
input
(2)f
input
(0)) / (ATs * m)
f
output
(2) = (f
input
(3)f
input
(0)) / (ATs * m)

If you enter an odd number
(K = odd):
f
output
(K) = (f
input
(K+1)f
input
(K 2)) / (ATs * m)

If you enter an even number
(K = even):
f
output
(K) = (f
input
(K+2)f
input
(K 2)) / (ATs * m)


Note: The online (real-time) Difference calculation is calculated differently because projected values are not
available. The online Difference formula is:
f
output
(n) = f
input
(n m)f
input
(n) / (ATs * m)
Using the default difference setting of 1 interval will produce a AP/AT waveform when the
transformation is applied to a blood pressure or similar waveform.


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Part C Analysis Functions 291
Resample

TIP A good rule of thumb is to sample from two to ten times the highest frequency component of interest.
Variable sampling rate and the flexible acquisition speeds of MP units can create data sets that are at different
sampling rates. For some types of data analysis, the data must be resampled to a common sampling rate.
AcqKnowledge has resampling facilities with Transform > Resample Graph; Transform > Resample Waveform,
and Pasting between graph windows of different sample rates when the Interpolate pastings between graphs
Preference is enabled (via Display > Preferences, page 424).
AcqKnowledge provides three interpolation methods for resampling data. Any changes made to the interpolated
pastings between windows Preference and the interpolation method used in the Preferences dialog will be
retained across launches of the software.
PaddingPadding will use the closest original value of the waveform to the left of the new sample
position for the value, constructing a padded square save as the data is resampled. Padding is desirable
when it is imperative no new data or data approximations get introduced into an analysis.
LinearLinear interpolation is the default; previous software versions generated any missing data via
linear interpolation. This method uses the sample points of the old waveform as the endpoints of a line.
Missing data points are approximated from points lying on this linear segment.
Cubic splineCubic spline interpolation will construct a spline for the entire data set and use the values of
this spline as the new waveform values. A natural fit spline is used that keeps zero second derivative at the
endpoints of the fit. Cubic splines are useful when the analysis requires data with a smooth derivative.
Resample Graph
Apply an arbitrary, user-defined sample rate to all graphs in the file.
The highest rate you can enter is the Acquisition Sample Rate.
This option will adjust as necessary to maintain the established channel rate/acquisition rate proportion.
You can create channel-specific rates by changing the channel sample rate after Resampling.
Resample Waveform
Resamples the active channel to a different rate. Resampling data maintains the same time scale but changes
the number of samples per second. You can also use Resample to increase the number of sample points per
interval (usually samples per second). When this is done, AcqKnowledge will interpolate between sample
points to adjust to the new rate. This will add data points, although not necessarily more information.
Resampling to a lower sampling rate will compress a data file and information will be lost.
For instance, a 4-channel data file sampled at 250 samples per second for 15 minutes takes up about
1.8 MB of disk space. If these channels are resampled to 100 samples per second, the size of the file
on disk is about 720 KB, a considerable reduction
The highest rate a channel can be resampled to is the file acquisition rate (MP menu > Set Up
Acquisition).
If data is resampled to a lower rate and then resampled again at a higher rate, the waveform will
maintain the resolution of the lower sampling rate, only with more data points.
The alpha component of an EEG signal has a frequency signature of 8-13Hz, so (assuming you have isolated
the alpha component using a band pass filter) you would probably want to sample the data (in this case, isolated
alpha waves) at a rate of at least 26Hz and probably no more than 130 Hz.
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Expression


See the tables on page 140 for descriptions of sources, operators and functions for the Expression dialog.
The post-acquisition Expression transformation is available for performing computations more complex than
available with the Math and Function calculations. The post-acquisition version of the Expression
transformation includes all the same features as the online version described on page 136. The Expression
transformation will symbolically evaluate complex equations involving multiple channels and multiple
operations. Unlike the Math and Function calculations, which can only operate on one or two channels at a
time, the Expression transformation can combine data from multiple analog channels, or specify other
calculation channels as input channels. Also, computations performed by the Expression transformation
eliminate the need for chaining multiple channels together to produce a single output channel.
To have AcqKnowledge solve an equation/expression and save the result to a new channel, choose Transform >
Expression. A dialog will be generated. For each equation/expression, specify a source channel (or channels),
the function(s) to be performed, any operators to be used, and a destination for the result. The different
components of each equation/expression can be entered either by double-clicking items from the pop-up menus
(sources, functions, and operators) in the setup dialog, or by typing commands directly into the box using
standard mathematical notation.
Any expression can be assigned a specific name and saved as a custom preset. A pop-up menu of recently used
expressions is also available in the Preset menu, along with a pre-loaded list of commonly used expressions.
You can divide a complex equation into several steps and perform each part of the equation with a separate
channel. With up to 60 channels, almost any calculation can be performed.
The Expression transformation can reference past and future points.

Delay
The Delay transformation allows the addition of time delays in postprocessing (similar to the Delay calculation
channel that can be used to add time delays to signals). The time delay can be added by introducing zero-valued
samples at the start of the area to be delayed. The length of the waveform will remain the same; an amount of
data at the end of the wave prior to the delay will be lost, with the length equal to the delay. The delay can be
applied by using the Transform > Delay menu item.

When inputting the delay amount, the units can be changed between seconds and samples.
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Part C Analysis Functions 293
- Delay by samples is applied according to the acquisition sampling rate, not the channel sampling rate.
Delay specifies the units of acquisition and graph sampling rate for samples.
- For Delay calculation channels, the units of samples need to be kept constant under changes to the
channel sampling rate as there is no opportunity to adjust them. As a result, acquisition sampling rate is
used to determine samples for calculation channels. This same logic is applied to the transformation.
The Automator action allows Delay to be used in Automator workflows. See page 24.
Rescale
The Rescale transformation operates the same as the Rescale calculationsee page 150.

Waveform math

The Waveform math transformation allows arithmetic manipulation of waveforms. Waveforms can be added
together, subtracted, multiplied, divided or raised to a power. These operations can be performed using either
two waveforms or one waveform and an arbitrarily defined constant. You can operate on the entire waveform
by choosing Edit > Select all, or operate on portions of the waveform that have been selected using the cursor
tool. If there is no selected area, only one sample point (the one selected by the cursor) will be transformed.
When you select Transform > Waveform Math, the Waveform Arithmetic dialog will be generated.
All of the main components of a waveform math calculation can be selected from pop-up menus in the
Waveform Arithmetic dialog.
Source The channels to be used in the transformation are referred to as source channels (Source 1 and
Source 2), and can be combined using any of the operators in the pop-up menu. Source
channels allow you to select any of the existing channels in the current window, or a constant
(defined by K).
Constant The Constant = entry box is activated when a Source is set to K, Constant.
Operand The pop-up menu allows selection of addition, subtraction, multiplication, division or power
functions.
Destination You can save the results to an active channel, or create a new channel to store the results.
Choose an existing channel from the pop-up menu or select the New option, which will
create a new channel (using the next available channel).
Result sample When using variable sample rate processing, the Expression transformation and Waveform
Rate Math functions will constrain operations between waves of different rates as follows:
If an equation is operating on two or more waves of different sample rates, the result of
the operation will always be output at the lowest sampling rate from the waves (F low).
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If the destination channel for the result has an assigned rate other than (F low), the
operation will not be permitted.

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If the destination channel is set to a new channel, the operation will always be
permitted.
Scaling Generates the scaling parameters dialog.
Waveform math can be used many ways. As one example, two waveforms can be added together. The
following screen shows a sine wave in channel 14 and a triangle wave in channel 16.

To add these two waves, select Transform > Waveform Math and set source 1 to channel 14, the operator to
addition +, source 2 to channel 16, and destination to New as shown here:

Click OK to perform the transformation. The following screen shows the sum of CH14 and CH16 on a new
channel.


NOTE: If you select two waveforms of unequal length as sources, the length of the resulting
waveform will be equal to that of the shortest one. Likewise, if one of the source
waveforms extends only into a portion of the selected area, the resultant waveform
will only be as long as the shortest source portion. If waveform math is performed on
a selected area and output to an existing waveform that does not extend into the
selected area, the resultant waveform is appended to the destination waveform.

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Part C Analysis Functions 295
Chapter 16 Analysis Menu Commands
Overview
The Analysis menu contains operations that derive data and measurements from the graphplus a courtesy
copy of the Specialized Analysis package with classifiers and automation routines.

Histogram

The Histogram function produces a histogram plot of the selected area. When a histogram is created, the sample
points are sorted into bins along the horizontal axis that contain ranges of amplitude values. These bins divide
the range of amplitude values into equal intervals (by default, ten bins) and the individual sample points are
sorted into the appropriate bin based on their amplitude value.
For instance, if a waveform had a range from 65 BPM to 85 BPM, the lowest bin would contain all data points
with a value from 65 BPM to 67 BPM. The second lowest bin would hold all data points between 67 BPM and
69 BPM, and so on, until the tenth bin was created. AcqKnowledge then counts the number of hits (the
number of data points) in each bin and plots this number on the vertical axis.
Analysis > Histogram Options:
bins Determines how many bins the data will be divided into; the default is ten bins.
Autorange Fits all the data selected into a bin; the bin sizes are determined by the extent of the data and the
desired number of lines. Automatically sets the center of the lowest bin equal to the minimum
value of the waveform (or the selected area, if a section is highlighted), and centers the highest
bin on the maximum value of the waveform (or selected area, if any).
Disable to fix the bin sizes and enter values for Highest Bin and Lowest Bin.
When you click OK, a histogram plot will be generated in a new window. By default, AcqKnowledge displays
the frequency of occurrence for each bin on the vertical axis. To calculate the cumulative frequency, select the
entire histogram waveform and choose Integrate from the Transform menu.
Since the histogram function sorts sample points into a relatively small number of categories, the histogram
window is likely to display a large number of hits in each bin, especially if data was collected at a relatively
fast sampling rate. If this is the case, you may want to resample the data at a lower rate (using the Transform >
Resample function). The caveat to this is that resampling the data may cause a bias, unless the data was filtered
to remove all frequency components that are more than 0.5 the resampling rate.

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Autoregressive Modeling
About autoregressive modeling
Autoregressive Modeling is a linear mathematical modeling algorithm that represents a signal as a
weighted sum of its previous values combined with a noise factor. Autoregressive models are adept at
capturing frequency behavior of an input signal and may be useful in generating high-resolution FFTs
from undersampled data.
AR models are well suited to operation on discrete series of data and are particularly useful for
expressing frequency information of a signal. Consecutive models can be used to perform advanced
time series analysis, compression, denoising, arrhythmia detection, and waveform classification. AR
models are commonly used on physiological data in advanced spectral analysis, and increasingly for
classification of heart rhythms and gastric waves or visual detection of arrhythmias.
AR models can be used to extrapolate spectral features from waveforms at low sample rates.
Generate high-resolution FFTs without fast acquisition sample rates (quite useful for
electrogastrogram analysis).
An FFT from a 3,000-point AR Model provides the same result as a 42,000-point FFT.
Examine spaces of AR parameters for feature extraction.
Since the underlying model is linear, AR modeling is not appropriate for representing signals that are
inherently chaotic.

AR Time-Frequency Analysis is on page 299.
Autoregressive modeling estimates the parameters of a
fixed-order autoregressive model, representing a
model output value as a linear sum of previous input
values. AR modeling may replace the source data with
the model of equivalent length. The output length is
equal to the source data, unless specified.
Output can also paste model parameters as tabular text to a journal. If Dont modify waveform and Show
model in separate graph are both enabled, a new graph window will be generated to display the specified
number of samples resulting from the best-fit autoregressive model.

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Part C Analysis Functions 297
Nonlinear Modeling
About nonlinear modeling
Modeling is used in physiological data to assess how well data conforms to a theoretical model. This is
used to express a sampled signal in a continuous form and to perform data reduction. The nonlinear
modeling features in AcqKnowledge support more advanced physiological analysis than is possible with
the linear regression measurement, which is a rudimentary single order linear model.
Nonlinear modeling is the process of finding the best fit of a mathematical function to an arbitrary data
set. Fitting the functionor modelto the data consists of choosing a set of function parameters that
minimize error between the actual data points and the values generated from the model function.
Nonlinear modeling functions can be arbitrarily complex. When the model is close to the shape of the
data, the fits between different data sets may be good indicators of subtle variations in the data.
Most general-purpose methods of performing modeling are iterative and require an estimator for the
function. A commonly used estimator is the least means squares (LMS) estimator. Nonlinear models can
be estimated from data by combining LMS estimators with multidimensional function minimization
algorithms.
Applications in hemodynamics
Many pressure and ECG signals exhibit regular morphologies. Fitting data to models that share these
characteristics helps emphasize subtle differences in waveforms though variations in their model
parameters. Nonlinear modeling is one of the most accepted methods for computing indexes for the
relaxation period of left ventricular pressure. Cardiac researchers have used the time constant tau
in various studies on cardiac function and abnormalities. Tau is determined by one of the parameters
to an exponential model of the trailing end of the pressure signal. Studies have indicated that tau can
be a good indicator of cardiac dysfunction, but reliable methods for its calculation have proven difficult
and the effort is ongoing. The generic modeling abilities in AcqKnowledge allow researchers to
analyze data using the tau constant and potentially develop robust algorithms for its calculation.
See the NLM measurement on page 100
Nonlinear modeling (also called arbitrary curve fitting)
determines the best fit of an arbitrary function to
source data; the function is called a model.
AcqKnowledge uses a Nelder-Mead simplex search with
a Euclidean distance function. A model must match
underlying trends in the data to produce meaningful
results. Also, to properly interpret the value of the best fit
coefficients and any further derived results, users must
consider the limitations of the simplex search method,
which include: estimation only; not guaranteed to
terminate; not guaranteed to find the exact solution; may
get stuck in local minima.
Nonlinear modeling generates a new display and replaces source data with a model of equal (unless specified)
length and also pastes model parameters as text to a journal. The sampling rate and axis units match the source
graph.
Max iterations
Indicates the number of iterations after which the simplex search will be terminated if no convergence has
been achieved.
Tolerance
Provides the tolerance used for termination of the algorithm. If the estimator decreases in two consecutive
steps by less than this tolerance, the simplex search will halt.

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Model origin placement
Controls where the zero point of the model is placed. Selection-relative placement is useful when comparing
different sections of the same channel of data by looking for variations in their best fit model parameters. If
channel data is used as part of the Model Expression the location from where the channel data is extracted
will not be translated; regardless of the model origin setting, the channel data will be used from the selected
area only.
Model Expressions
Models are defined through basic expressions, called Model Expressions. See the function tables starting on
page 140 for details on Sources, Functions, and Operators.
Preset
The following presets for the most common types of models are included. Users can extend presets or create
custom models if these presets are too general to achieve exact fits with simplex search. Presets are stored at
Computer > Local Disk > ProgramData > BIOPAC Systems, Inc > AcqKnowledge 4.0 > Presets.
Preset Description Equation
Cubic 3rd order polynomial. param(3)*(TIME^3)+param(2)*(TIME^2)+param(1)*TIME+param(0)
Gaussian Standard Gaussian model; useful
for peak fitting.
param(0)*EXP(-((TIME-param(1))/param(2))^2
Linear Basic linear fit of the data. param(1)*TIME+param(0)
Logarithmic Logarithmic growth and decay;
useful for initial rapid growth/decay
followed by gradual
decline/increase.
param(0)*LOG(TIME-param(1))+param(2)
Logistic Logistic LVP relaxation model;
T
L
given by a(1).
param(0)/(1+EXP(-TIME/param(1)))+param(2)
Monoexponential Exponential LVP relaxation model;
T
e
given by a(1).
param(0)*EXP(-TIME/param(1))+param(2)
Power Series Useful for a wide variety of data,
e.g. reactant analysis.
param(0)+param(1)*(TIME^param(2))
Quadratic 2
nd
order polynomial. param(2)*(TIME^2)+param(1)*TIME+param(0)
Weibull
Distribution
Commonly used in reliability
analysis.
param(0)*param(1)*TIME^(param(1)-1)*EXP(-param(0)
*TIME^param(1))
Sources
All channels except the channel being modeled can be used as Sources; if the channel of data being modeled
is inadvertently set as a Source, a syntax error prompt will be generated.
Parameters
Parameters are represented by param(n) where n is an integer index starting from zero. For example, in the
linear model param(0)*x+param(1), param(0) can be interpreted as the a in ax+b and param(1) can be
interpreted as the b in ax+b.
Output to Journal displays the result of the modeling as text in the journal.
Show model in separate graph generates a separate graph to display the best fit model.
Length specifies the length of the separate model graph in samples.
Dont modify waveform suppresses replacement of the selected source data.
If the model fitting does not complete successfully, the original data will be preserved regardless of
the state of this selection.
Transform entire wave
Fits the entire data of the selected waveform to the model, with model origin at start of graph.
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Part C Analysis Functions 299
Power Spectral Density
The Power Spectral Density (PSD) function extracts the
power present at different frequencies within a signal and is
useful for EMG analysis. The PSD transformation
approximates the same result as squaring the linear FFT
magnitude. PSD is not available when the horizontal units
of the source graph are set to Frequency.
AcqKnowledge uses the Welsh approximation algorithm to
average signal time-sliced portions of the signal and reduce
noise effect, and generates a two dimensional graph
displaying the wattage of a particular frequency component
in a signal. Windowing options are Hanning, Hamming, or
Blackman. The graph is plotted as horizontal frequency vs.
vertical (units)^2/Hz, where units are the vertical axis units
of the source data.
Use linear detrending for each windowwhen enabled, linear regression detrending is applied for each
individual segment prior to the FFT computation; when disabled, windowing only is applied.
Detrend each segment independentlybecomes available when Use linear detrending is enabled. When
this option is enabled, detrending is applied independently for each segment; when disabled, detrending from
the previous segment will be incorporated into the next segment.

AR Time-Frequency Analysis

The AR Time-Frequency transformation can be used to
examine changes in the spectral density of a signal using
enhanced frequency resolution from derived AR models.
Examining frequency changes over time can be a useful tool
for arrhythmia detection and rough classification of
waveforms.
Autoregressive spectrum time-frequency analysis divides a
waveform into equal-length time segments, calculates an AR
model (see page 298) for each individual time segment, and
then computes a power spectrum from the model. (To perform
raw data time-frequency analysis, use the Cycle/Peak detector
with the FFT 3D output option.)

Time intervalEnter a positive floating point value to specify the segment width; the source signal is split into
fixed length segments of this width and a frequency spectrum is generated for each segment from a model of its
data.
Model orderEnter a positive integer to specify the order of the AR model that is constructed on an interval
by interval basis.
Frequency resolutionEnter a positive integer to indicate the number of points contained in the FFT of an
individual time segment; it will be rounded to the closest power of 2 when analysis is performed.
Amplitude scalingNormalize amplitudes scales amplitudes such that the maximum peak-peak distance is
equal across time intervals.
Show 3D OutputConstructs a 3D surface plot of the time-frequency analysis with amplitude vs. frequency
vs. time.
Paste results to journalInserts a series of tab-delimited tables representing the frequency distributions on a
cycle-by-cycle basis into the Journal.
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FFT Fast Fourier Transformation

The FFT algorithm requires that the length of your data be an exact power of
two (i.e., 256 points, 512 points, 1024 points, and so on).
The Fast Fourier Transformation (FFT) is an algorithm that produces a description of time series data in terms
of its frequency components. This is related to the frequency spectrum. The FFT displays the magnitude and
phase of the time series data selected and displays only the DC and positive frequency components; the FFT
does not display negative frequency components. To reconstruct a signal from additive sines or cosines, you
need to include both the positive and negative frequency components. Since its not physically possible to
generate a negative frequency signal, you need to double the amplitude of the corresponding positive frequency
component.
The output from an FFT appears in a graph window with magnitude (vertical axis) plotted against various
frequencies (horizontal axis). A large component for a given frequency appears as a positive (upward-pointing)
peak. The range of frequencies plotted is from 0 Hz to 1/2 the sampling frequency. Thus, if data was collected
at 200 samples per seconds, AcqKnowledge will plot the frequency components from 0 Hz to 100 Hz.
Fourier analysis can yield important information about the frequency components in a data set, and can be
useful in making determinations regarding appropriate data cleaning techniques (e.g., digital filtering). The FFT
algorithm assumes that data is an infinitely repeating periodic signal with the end points wrapping around. Thus,
to the extent that the amplitude of the first point differs from the last point, the resulting frequency spectrum is
likely to be distorted as result of this start point to end point discontinuity. This can be overcome by
windowing the data during the transformation. For more information on the windowing feature, see the
window section that follows.
The FFT transformation cannot be performed in real time (i.e., during an acquisition). To emulate an online
spectral analysis, use online filters and the Input Values window. See page 218 for more information about real-
time frequency information.

Pad If a section of data is selected that is not a power of two, AcqKnowledge will always pad data
up to the next power of two, filling in the remaining data point with either
Pad with zeros: a zero
Pad with last point: the last data point in the selected area
In other words, if 511 data points are selected, AcqKnowledge will use a modified version of
the waveform as input. The modified waveform will have 512 points, and the last point in the
modified wave will be either a zero or equal to the 511
th
point of the original data.
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Part C Analysis Functions 301
Show Mod. To view the modified waveform being used as input for the FFT, check the Show modified
input box. Whenever possible, it is best to use an input waveform (select an area) that is an
exact power of two. The waveform is modified by applying the windowing and padding
options. Window functions diminish the discontinuities that occur at either end of the wave.

Window The FFT algorithm treats the data as an infinitely repeating signal with a period equal to the
length of the waveform. Therefore, if the endpoint values are unequal, you will get a frequency
spectrum with larger than expected high frequency components due to the discontinuity.
Windowing these data minimizes this phenomenon. For example, to apply a window
transformation to a sine wave whose endpoints do not match up, check the box next to Window
and choose a type of window from the pop-up menu. Each of the windows has slightly different
characteristics, although in practice each provides similar results within measurement error.
As shown below, the frequency spectra of the windowed and non-windowed data differ
significantly when the endpoints are unequal. When data are not windowed, the very low and
very high frequencies are not attenuated to the same extent as when windowed.

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Remove Sometimes, data contains a positive or negative trend that can cause extraneous
Trend frequency components to leak into the frequency spectrum. In this case, you could select
remove trend when you perform the FFT, which will draw a line through the endpoints, and
then subtract the trend from the waveform.
For example, the
following sine wave
has an upward trend
through the data
(positive trend
component). The lower
graph shows FFTs of
the skewed sine wave
data with and without
the trend removed.
Note that the spectrum
of the data without the
trend removal has
gradually decreasing
frequency components,
while the data with the
trend removed has far
fewer frequency
components except for
the single spike due to
the sine wave.

without trend removal
trend removed

Remove Mean Remove mean calculates the mean of all the points in the selected area and then subtracts it
from the waveform. This is generally useful for windowing a waveform that has a large DC
offset.
As an example, you might start with a sine wave with a 10-volt DC offset (with a little noise
added to broaden the spectrum), and perform spectral analysis with and without mean removal:

Note the large spectral components at the beginning of the top plot, without mean removal.
This is due to the offset of the original data. The bottom plot is with mean removal.
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Part C Analysis Functions 303
Since the offset of the waveform is often an artifact of the way it was generated, the remove
mean option provides a more accurate indication of the true spectral components. This is
especially true for applications where low frequency components are of interest. If your data
has a large DC offset and you plan on windowing the data, you will generally get a more
meaningful spectrum if you remove the mean prior to windowing (which is the same order the
FFT uses).
Linear By default, the FFT output is described in terms of frequency along the horizontal axis and
dBV on the vertical axis. The Bell scale (from which dB are derived) is logarithmic, and in
some cases it may be useful to have the output scaled in linear units. To do this, click the button
next to linear and check OK. The other options in the dialog work as they normally do when the
dB scaling option is selected. The relationship between log and linear units is: dBV
out
= 20 log
VIN.
Phase The standard FFT produces a plot with frequency on the horizontal axis and either dB/V or
linear units (usually Volts) on the vertical axis. In some cases, it may be useful to obtain phase
plots of the waveform (as opposed to the default magnitude plots). Phase plots display
frequency along the horizontal axis, and the phase of the waveform (scaled in degrees) on the
vertical axis. This option functions exclusive of the magnitude optionyou can check either
independently, or if you check both, two plots will be produced (a magnitude plot and a phase
plot).

Inverse FFT

The Transform > IFFT menu option is generated after an FFT is
performed. An Inverse FFT (Transform > IFFT) converts spectral
values back to a time series waveform to reverse the FFT
transformation. Any modifications to the original data (such as
windowing or padding) will be shown in the resulting time series
data.
To obtain a meaningful IFFT result you must have a graph window
open with at least one magnitude channel and at least one phase
channel. With the window open, choose IFFT from the Transform
menu to generate the Inverse FFT dialog.
To accurately recreate the time series waveform
1. Select the source channels for the inverse FFT in the Magnitude and Phase pull-down menus.
2. Select whether to express Magnitude in linear units or dB logarithmic units (decibels). To determine
this setting, check the vertical axis units of the magnitude channel; this should correspond to the
Magnitude scaling choice that was used when performing the forward FFT.
The Phase waveform must be in degrees.
3. Click OK to perform the IFFT.
The result is generated in a new time domain window, labeled IFFT of Spectral
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To perform an FFT, you might start with an electroencephalogram (EEG) signal acquired when the
subject alternated between eyes open and eyes closed. Typical results suggest that higher levels of alpha
activity (activity with frequency components between 8Hz and 13Hz) are to be expected when a subjects
eyes are closed.
1. The raw data, prior to FFT, is shown here:

Eyes
open
Eyes
Eyes
open
closed

2. Select Transform > FFT from the menu.
The FFT Parameters dialog will be
generated; in this example, the Window
function chosen is Kaiser Bessel:

13107
3. Click OK.
A frequency domain window (a graph
window which places frequency along the
horizontal axis rather than time) will be
created and displayed, showing the spectrum
of the input data.
The window is named Spectral of (the
original window name) and ends with the
channel number, as shown here:
The resulting magnitude value for each
component is equal to the peak value of the
sine wave contributing to that component.
The entire pattern of frequency components
is known as the frequency spectrum of the
data. The somewhat erratic appearance of the
spectrum is usually due to small-scale
variations in the original waveform.
4. OptionalThis noise can be removed by
applying a smoothing transformation to the
FFT output. In the graph shown, there is a
pronounced frequency component centered
on 8Hz, which corresponds to the alpha wave
frequency band (8Hz13Hz). The frequency
spectrum (0-20 Hz shown) used 20-point
smoothing.









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Part C Analysis Functions 305
DWT Discrete Wavelet Transformation

About Wavelet Transformation
Wavelet transforms are similar to Fourier transforms. Instead of
projecting a signal in a space of sines and cosines, wavelet transforms
project a signal into a space comprised of orthogonal functions called
wavelets. Discontinuities are more obvious in wavelet transforms than in
sines and cosine analysis, making wavelet transforms a better choice
for decomposing a signal to its fundamental form. Wavelet transforms
can be used for noise reduction and filtering, extracting features from
signals that are not apparent in time or frequency domains, and
predicting signal qualities from a small number of data points.
Discrete wavelet transforms break a source signal into high-frequency and low-frequency components. Use for
ECG and EEG analysis. DWT creates a new graph with wavelet coefficients on the horizontal axis and the
amplitude for each coefficient on the vertical axis, pastes acquisition settings to the graph-specific journal, and
places an event at each boundary between the high- and low-frequency components produced at each iteration.
Wavelet type Specify Biorthogonal 4.4, Symlet 4, Coiflet 6, or Daubechies 8.
Number of iterations Specify the number of transforms to execute iteratively.
Inverse DWT
Operational on the result of a DWT. Projects data from wavelet
space to time space. For correct recomposition of the source
data, the wavelet type specified for the IDWT must match the
wavelet type used for the DWT. Amplitudes of the wavelet
coefficients may be changed, but an IDWT will fail if the
horizontal units, events at DWT iteration level boundaries, or
file length have been modified.

Principal Component Analysis
About Principal Component Analysis
Principal Component Analysis decomposes source signals into a
new signal space (constructs an orthogonal set of vectors). PCA is
useful as a feature extraction and data reduction tool.
Changes in the values of the mixing matrix may be indicative of
changes in underlying signal morphologies that other methods
cannot easily detect.
For example, PCA is useful for EEG analysis; where it can reduce
32 channels to the fundamental elements of signals.
AcqKnowledge uses a mean-adjusted covariance matrix method to generate a new PCA graph with each
component in a separate channel. The coordinates of the new space are the eigenvalues extracted from the
matrix defined by the source data and are called Principal components. The extracted eigenvectors are the
mixing matrix. Sine and cosine are orthogonal signals. The principal components are numbered in order of
decreasing eigenvalues, which implies that the first principal component contains the majority of the variation
of the source signals. Results are also pasted in to the journal, including the eigenvalue magnitudes and the
eigenvector matrix. To determine the percentage contribution of each component, review the eigenvalue
magnitudes. Select two or more channelsall of the selected channels must have the same sampling rate.
Inverse PCA
Available only for graphs produced by PCA. Reconstructs the source signals based on the components and
mixing matrix of the PCA graph. The graph is reconstructed in a new window, with a list of the components
used pasted to the journal.
C For noise reduction, use only the strongest principal components to reconstruct the source signals.
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Independent Component Analysis

About Independent Component Analysis
Independent Component Analysis is useful for signal separation,
denoising, and advanced EEG analysis to remove noise signals or
locate approximate regions of active processing centers in the brain.
ICA is a form of statistical blind separation that attempts to separate
mixed (overlapped) signals based on the assumption that they are
statistically independent.
For example, if two microphones in a room record one person
reciting Shakespeare and another person playing the banjo, the
recordings will capture both the speaker and the banjo. After
performing ICA on the two recordings, one result will have only
the speaker and the other will have only the banjo.
AcqKnowledge uses the FastICA algorithm to generate a new ICA graph with each component in a separate
channel.
Select two or more channelsall of the selected channels must have the same sampling rate.
Specify tolerance and number of iterations.
ICA limitations to consider for application and interpretation:
1. The number of mixed sources must be equal to the number of independent components (as in the
example where two microphones captured two sound types).
2. Sources must be statistically independent; highly-correlated signals cannot be effectively separated.
3. Sources must have non-Gaussian probability distribution. It is not possible to separate out components
like white noise through ICA.
4. Signal mixing must be a constant, linear process. Any type of non-linear signal propagation cannot be
expressed in linear combinations of sources, the underlying assumption of ICA.
5. The component sources must be stationary (that is, point sources).

Inverse ICA
Available only for graphs produced by ICA. Reconstructs mixed signals based on the components and
mixing matrix of the ICA graph. The statistical nature of the algorithm implies that it cannot perfectly
reconstruct original source datait estimates the most probable set of source signals. The graph is
reconstructed in a new window, with a list of the components used pasted to the journal.
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Part C Analysis Functions 307
Find Cycle (Peak Detector)

The Find Cycle/Peak Detector setup dialog is accessed by choosing Analysis > Find Cycle, clicking the toolbar
icon , or using the Ctrl-F keystroke.
Overview
The advanced Cycle/Peak Detector combines with the powerful new Event Marking System. Use it to perform
amplitude, time, or event-based measurements. New output options for measurements, averaging, events,
clustering (K-means), and 3D surface (cycle data, histogram, FFT, and DWT).
The Find Cycle detector uses three tabbed settings panels to define and automate cycle/peak detection:
Cycles/Peaks Selection Output
Cycle detector settings are graph-independent, which means that find cycle/peak operations can be performed
in multiple graphs without needing to re-enter graph-specific settings for each run. By using multiple data
views, different find cycle/peak operation can be performed on the same set of data without losing settings
between Find Next Cycle/Peak operations.
When the Cycle/Peak Detector is first opened for a graph, the dialog will be filled with the values from the last
successfully executed find Cycle/Peak operation. Subsequently, changes to the settings will be applied only to
that graph.
TIP If you're running the cycle/peak detector multiple times and need to put the edge back at the
beginning of the waveform for the next pass, use the keyboard shortcuts Home, End, Page Up, and
Page Down to quickly change edge location (see page 63).
Cycles/Peaks tab

Peaks Events

Fixed Interval
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Find Cycle controls available at bottom of dialog
Find Next Cycle
When selected from the Analysis menu (or select the toolbar icon or Ctrl+E), both edges will move one
peak to the right while staying above the threshold.
Find All Cycles in Graph
When selected from the Analysis menu, Find Cycle setup dialog or selecting Ctrl+R,, the software will find all
cycles/peaks through the end of the file. If your data file is very large, it may take some time to find all the
cycles since AcqKnowledge loads data from disk while it scans for the cycles.
Find in Selected Area
When selected from the Analysis menu or in the Find Cycle setup dialog, only cycles within a selected area will
be detected, all others will be ignored.
Find All Cycles in Focus Areas
If the graph contains defined focus areas, this option will limit cycle detection to focus areas only. If no focus
areas are defined, this option will not be available. This is selectable via the Analysis menu or in the Find Cycle
setup dialog.
Find First Cycle
Use this option to apply changes to the Find Cycle setup and locate the first cycle. This is selectable via the
Analysis menu or in the Find Cycle setup dialog.
Preview
When selected, a preview of the selected Find Cycle operation is displayed prior to applying the settings.

Find Cycle definitions
A cycle is defined as the interval between two events of user-
specified types. The Cycles/Peaks tab offers three general
methods for establishing cycle parameters:
Peaks: Data driven maximum and minimum
Events
User-defined fixed time intervals
When the cycle location mode is switched on the Cycles/Peaks tab, the edge selection offsets will be checked.
If they are non-zero, a prompt will generated to warn that that the edge adjustment offsets may not apply for the
new cycle location mode. The user can reset the offsets to zero (default) or retain the (non-zero) settings used in
the previous cycle location mode.
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Part C Analysis Functions 309
Peaks
Peak direction See the Peak definitions.
Level Important usage noteLevel is not set automatically when the Cycle/Peak detector is
generated. (Automatic Level is used in previous versions of AcqKnowledge for Mac and
current version for Windows.)
Use selected... To optimize the threshold detection level for the selected area of data in the graph, click the
Use selected maximum/minimum button underneath the level. If you change the source
channel or peak direction, you can also use this button to re-compute the recommended level
based upon your new settings. The recommended level is computed as per 'Tracking using %
of peak value' (see below) using a percentage factor of 75%.
Threshold FixedKeeps the threshold voltage level constant.
Tracking The Tracking threshold mode modifies the threshold after it finds a peak, depending upon the
value of the new peak, and will compensate for a slowly drifting baseline.
Hints regarding the use of Tracking Threshold Options
- If data has a very consistent cyclical nature, either Tracking Option will work.
- If data has spurious positive or negative peak values present, the Means Reference
Tracking Option is probably a better choice.
- If data has an erratic baseline, but consistently sized, positive and negative peaks, the
Peaks Reference Tracking Option is probably a better choice.
Tracking using mean value and % of peak valueAdjusts the threshold voltage level after
each peak based on the average of the last cycles data and the specified percentage of the
current peak voltage. The Means reference option will cause the software to determine the
Mean Value of all the data, from peak to peak. This Mean Value establishes a variable
reference upon which the tracking threshold operates. The software will determine the new
threshold (NT) as follows:
For Positive Peaks
NT = Mean Value + (Positive Peak Value - Mean Value) x (% factor)
For Negative Peaks
NT = Mean Value - (Mean Value - Negative Peak Value) x (% factor)
Tracking using % of peak valueAdjusts the threshold voltage level dynamically based on
the specified percentage of the value of the most currently found peak. The Peaks reference
option will cause the software to determine the Positive Peak Value and Negative Peak Value
of all the data, from peak to peak. The Positive and Negative Peak Values establish a variable
reference upon which the tracking threshold operates. The software will determine the new
threshold (NT) as follows:
For Positive Peaks
NT = Neg. Peak Value + (Pos. Peak ValueNeg. Peak Value) x (% factor)
For Negative Peaks
NT = Pos. Peak Value - (Pos. Peak ValueNeg. Peak Value) x (% factor)
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Events
Event-based cycle location can extract information from events or define events based upon the output of the
peak detector. A cycle is defined as the interval between two events of user-specified types.
Start / End Define the event; any of the predefined event types can be explicitly matched.
Match pairs Match pairs of events only is active when the Start event criteria are identical to
the End event criteria. Toggle the checkbox to set this option. For a cycle to be
located, a pair of two distinct events that match the criteria must be present. The
event occurring earlier in time matches the left edge, later in time matches the
right edge. This is the default search mode; this is the only search mode when the
criteria are different.
When unchecked, a single event can be used as the Start event and the End event
of a cycle, which will produce a zero width cycle. This is useful for adjusting a
selection relative to an event, such as locating the first second prior to each event
of a specific type. This single-event matching option makes it possible to hit time
periods for each event since each cycle consumes two events.
Located on Specify the channel when the event must be defined, either its actual channel or
Global for events not associated with any channel. Select Anywhere to search
for events of specific types across channels.
With Labels
optional
Toggle the With labels containing text checkbox to set this option.
When checked, the matching events label must contain the text in the edit box to
the right of the checkbox.
The text search is not case sensitive. The search must be non-empty for cycles
to be located properly.
When unchecked, the matching event can have any label, including none.
The Cycle detector uses the following algorithm to search for cycles in the graph:
1. From the starting point, find the first event matching the criteria of the Start event. This will be defined
as the left event. If no event matches the Start criteria, no more cycles are in the file.
2. If the Start event criteria match the Ending event criteria and zero width cycles are allowed (e.g. Match
pairs of events only is unchecked), define the right event as identical to the left event and go to step 5.
3. From the location of the left event, find the closest event matching the criteria of the End event. This
will be defined as the right event. If no event matches the End criteria, no more cycles are present in the
graph.
4. Within the time region between the left and right events, search for any events that match the Start
criteria. If such an event occurs, redefine the left event to be this matching event and repeat the step. If
no event is located, then the closest pair of events has been located.
This step is useful for working with data that has missing portions of the sequence, as can come out
of some classifiers. For example, if two event types A and B are used as the endpoints, a sequence
of three events AAB will match the last two events as the cycle. This is logical in the case of
physiological data where, if B should occur periodically in the signal, AA is an indicator of an
abnormality or missed classification.
5. Set the selected area to the time interval whose endpoints are the left and right events.
6. Perform selection adjustment and output as indicated by the settings on the Selection and Output
tabs.
7. If Find All Cycles is being performed, return to step 1 and use the ending event location as the new
starting point to find any remaining cycles in the graph.
Fixed Interval
See the interval definitions.
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Part C Analysis Functions 311
Selection tab
Use the Selection tab to adjust the range of data that will be analyzed to generate any output. By default, the
data range is set to be the entire cycle as located by the settings on the Cycle/Peak tab, but it can be adjusted to
analyze only specific portions of the cycle.
The controls on the Selection tab vary based on the settings on the Cycle/Peak tab
Peak When the Cycles/Peaks location method is Peaks, you can adjust the Selection based on the
times of the peaks in the data or the times of the threshold crossings prior to the peaks.

To perform analysis on the entire data within each cycle, the selection should be from the
previous peak to the current peak. To examine fixed-width time windows located at each
peak, use the current peak to current peak settings and adjust the two time offsets
accordingly. Note that your settings must place the left edge earlier in time than the right edge
for the peak detection to succeed properly.

Move Cursor To Origin (at bottom left of screen) sets the graph data selection back to the first
sample. Use this to reset the cursor in order to find all of the data in the graph.
Event When the Cycles/Peaks location method is
Events, you can adjust the Selection
based on the locations of the events that
define the boundaries of a cycle.
For a specific cycle, the starting event will
be the event at the left boundary of the cycle
and the ending event will be the event at the
right boundary of the cycle. The starting
event will never be located after the ending
event in time.
To analyze data over each entire cycle, use the starting event to ending event setting. To
examine fixed-width time windows occurring within each cycle, set the left edge and the right
edge to the same event (e.g. starting event to starting event for time windows at the
beginning of each cycle) and adjust the offsets accordingly. Note that your settings must place
the left edge earlier in time than the right edge for the peak detection to succeed properly.
Fixed When the Cycles/Peaks location method is Fixed time
intervals, you can adjust the Selection based on the
endpoints of the time interval.
To analyze the data over each entire interval, use the
previous interval to current interval setting.
To examine fixed-width time windows within each
interval or only a sub-portion of each interval, use the
current interval to current interval setting and
adjust the time offsets accordingly. Note that your settings must place the left edge earlier in
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time than the right edge for the peak detection to succeed properly.
Output tab

The Cycle/Peak Detector includes six Output
options, which can be independently enabled:
Measurements, Averaging, 3D Surface, Events,
Focus Area and Clustering. The selected output, if
any, is listed at the top of the Output tab as Enabled
output.

Output Measurements
Toggle each checkbox to enable/disable the option:
Paste measurements for each cycle to
the Journal.
Plot measurement results; display
measurement values as channels in
graph.
Save measurements to Excel
spreadsheet file, plus output options. In
order for spreadsheet output to be
generated, a Find All Cycles
operation is required.
NOTE: If the horizontal axis is in world time
(HH:MM:ss,) any time measurement exported to
Excel will be reported in standard time units, such
as seconds or minutes.

Output: AveragingOffline
Use Averaging Output to perform offline ensemble
averaging of source data or ensemble averaging of event
locations. Specify the channel where the cycles/peaks
are to be located in the Cycles/Peaks tab and specify
the channel whose data should be ensemble averaged in
the Average controls on the Output tab.
Toggle the Average channel events checkbox near the
bottom of the tab to turn event averaging on and off.
Offline averaging can produce average locations of
events within the defined cycle along with the average
data. When a cycle is found, any events in that cycle will
be noted. Events that are on the channel of data being
averaged will be examined for inclusion in the average.
Index For each individual cycle, each event will be given an index starting at 0 and increasing to one less
than the number of occurrences of that event type within the cycle. The time offset for each event
from the start of its cycle will be averaged along with the offset for events with the same index from
all other cycles. When the graph of the averaged data is produced, these average time offsets from
the start of the cycle will be used to define new events for the averaged data. If the events and
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Part C Analysis Functions 313
averaging interval were correlated with the data, the average event offset will produce a reasonable
representation of the appropriate event locations for the averaged cycle.
Average events reflect the accuracy of classifiers and the consistency of data used to locate each
cycle.
Label Each event is labeled with the number of cycles contained in the event. Differences in the event
sequence can cause spurious events to be inserted. The label helps in manual inspection for events
that were only in one or two cycles.
Rejection Toggle the Events must be in checkbox to turn rejection on and off, and specify a percentage
for the relative number of cycles an event must appear in to be considered valid.
Remove When mean removal is enabled, the mean value of the data within each cycle is subtracted prior to
including it in the overall signal average. This mean removal option is useful for:
o Extracting signals that are riding on top of other signals with high DC offset (e.g., MRI
artifact on top of skin temperature)
o Compensating for baseline drift where there are not enough cycles present in the data for
the baseline variation to completely cancel itself out.
Output 3D Surface


Toggle the Generate a surface checkbox at the top of the 3D tab to turn Surface Output on and off.
1) Choose a channel to generate a 3D surface from.
2) Confirm or establish the cycle period of interest on the channel.
Use the Cycles/Peaks tab and the Selection tab to adjust the threshold and edge positions for the
cycle period for 3D output.
3) Choose a cross-section output format for the cycle data: cycle data, histogram, FFT, or DWT.
For histogram, FFT, or DWT, click Configure Transformation to change the settings.
4) Select surface and background colors.
5) Set axis options.
6) Click OK.
Use the cursor to rotate the 3D image; the magnitude of display response increases as you leave the center of the
screen (keep cursor close to center for slow response/display control).

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3D Output Example Compare ECG cycles in 3D Output. The following example shows how to
AcqKnowledge will generate a 3D image using each cross section of ECG.
a) Cycles/Peaks tab: set the threshold level to identify each R-wave.
b) Selection tab: set the edge to
Current Peak
Left edge -.5 seconds
Right edge .5 seconds
c) On the Output tab
Enable 3D Output
Specify the channel to generate a surface from.
Choose cycle data for the cross-section format.
d) Click Find All Cycles.
Output Events

Toggle the Output events checkbox at the top of the
Events tab to turn Event Output on and off.
The Cycle/Peak Detector Output mode can define
events at specific locations; a maximum of two events
per cycle can be inserted with Event Output. After the
Peak Detector has located a cycle and adjusted the
selection, the data within that cycle can be analyzed
and used to create new events in the graph (data-
driven or time specific).
Event definition

Insertion method &
channel selection
Brief definitions follow, see the Event Location table on page 315 for details:
At edge place the event directly at the specified edge (left or right). See Edge
Adjustment on page 315.
Percent change looks for a crossing based on a percentage of the value of the
signal at the corresponding edge and places the event when a signal increases or
decreases in value from the edge.
% peak to peak looks for a point where the signal's value has changed by a
percentage of the maximum peak-to-peak amplitude distance over the selected
area and places the event when a signal increases or decreases in value from the
edge
Minimum place events at the minimum of a specific channel's data within the
selection.
Maximum place events at the minimum of a specific channel's data within the
selection
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Part C Analysis Functions 315
The channel whose data should be examined is specified in the pull-down menu
directly to the right of the insertion method pull-down menu:
Output type
For each insertion method, the Output type pull-down menu adjusts the event
type of the inserted event.
Output channel
Sets the channel where the event is inserted, either Global for defining global
events or specific channels.
Nonedisables any insertion for that event and all of the other controls
will be hidden except the insertion method pull-down menu.
Left edge / Right edgea pull-down menu is displayed to be used to
change between the different offset methods
Minimum / Maximum
Output label
Use this edit field to type in specific label text. Each event that is inserted will
have its label set to this text. By default, it is empty (inserted events will not be
labeled).

Edge Adjustment When an at edge location method is used, options will be generated to fine-
tune event placement relative to that (right or left) edge of the selection.
Offset
Underneath the insertion method pull-down menu, a set of controls will be
added, allowing the user to specify the percentage, choose whether to search for
an increase or decrease, and choose the channel whose signal should be
examined.

When the offset method is Threshold crossing, the event will be placed when
the signal on a channel crosses a threshold.
There are a number of possible ways to configure the threshold crossing:
FixedThe edit field may contain a specific voltage level for the threshold.
In this configuration, an event will be placed if the value of the channel
specified in the next pull-down menu crosses this fixed voltage value.
+ valueThe edit field may specify an offset from the value of the channel
at an edge. The threshold voltage level is the value of the chosen source
channel plus the offset from the edit field. To specify a threshold lower than
the value of the channel at the edge, a negative sign can be placed before
the offset.
Direction of
crossing
The direction of the crossing can be specified.
+ (positive crossing)the signal must approach the threshold from below
and cross to above the threshold before an event is inserted.
- (negative crossing)the signal must approach the threshold from above
and cross to below the threshold before an event is inserted.
(mixed threshold)an event will be inserted at the first positive or
negative crossing that is encountered.
Event Location Table
Insertion Method Location Process
Edge, at edge Place an event at the left or right boundary of the selected area, as specified.
Edge +/- percent offset Given a particular channel, place an event at the specified time within the
selection when the signal increases or decreases by a specific percentage.
Left edge + Place at the time closest to the left boundary of the
selection. The percentage is calculated from the value of
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Insertion Method Location Process
the signal at the left boundary of the selected area.
Right edge - Place at the time closest to the right boundary of the
selection. The distance between the event and the right
edge of the selection will have an amplitude difference
equal to the indicated percentage of the right edges
value.
If the signal does not increase or decrease by that percentage within the
selection, no event will be inserted.
Edge +/- percent peak to
peak offset
Given a particular channel, place an event at the specified time within the
selection when the signal increases or decreases by a specific percentage of
the peak to peak delta of the selected area.
Left edge + Place at the time closest to the left boundary of the
selection. The percentage is calculated from the result of
subtracting the minimum value of the signal over the
selected interval from its maximum.
Right edge - Place at the time closest to the right boundary. The
distance between the event and the right edge of the
selection will have an amplitude difference equal to the
indicated percentage of the minimum value of the signal
over the selected interval subtracted from its maximum.
If the signal does not increase or decrease by that percentage within the
selection, no event will be inserted.
Edge +/- threshold
crossing
Starting at the specified boundary of the selection, determine a threshold
value. This threshold voltage may be:
fixed voltage level
value of signal at the specified edge + offset
mean value in selected area + offset
Left edge + Search for the first location where the signal on a
particular channel crosses the threshold.
Right edge - Examining data from right to left, search for the rightmost
location where the signal on a particular channel crosses
the threshold.
If the direction of the threshold crossing matches the user specified direction,
then an event is inserted. If it does not, then the next threshold crossing is
located and the process repeats. If the threshold is never crossed within the
selected area in the user-specified direction, no event is inserted.
Minimum The event will be placed at the time location corresponding to a specific
channels minimum value within the selected area.
Maximum The event will be placed at the time location corresponding to a specific
channels maximum value within the selected area.

Output Focus Area
Use this tool to define and highlight focus areas within the graph and include them in the Find Cycle output.

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Part C Analysis Functions 317
Define focus areas at selection boundaries
When checked, focus area output is enabled. Focus area selection boundaries will be defined as determined in
the Find Cycle selection setup.
Label basename
Use to assign a name or label to the cycles located in the focus area. The defined basename will appear in the
focus area section of the graph, along with incremented numbers for each subsequent cycle. (See below)

Output: Clustering
Clustering is the process of taking a set of data points and partitioning them into a fixed number of groups
called clusters. Each cluster represents data points that may share some type of commonality. This can be used
to assign each data point to a class of similar points. Clustering can be used for hemodynamic analysis and is
one of the basic analysis tools used for spike analysis in neurophysiology.
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Algorithm Overview
K-means clustering is an iterative algorithm that begins with a data set of real-valued points in an n-
dimensional space. Given this data set, one then specifies how many clusters are present. The k-means
clustering algorithm attempts to find the location at the center of each of these clusters. Essentially, this
algorithm partitions the data set into k groups such that the sum of the differences between the centers of
each group and its members is minimized.
A basic algorithm description is:
A. Given a total of k clusters, choose k potential cluster centers.
B. Assign each member of the data set to a cluster according to the closest potential cluster center
using a Euclidean distance function (sum-of-squares).
C. Adjust the location of the potential center for each cluster to a more optimal value. The most basic
method is to assign the new center as to match the mean value of all of the members of the set
(referred to as expectation maximization).
D. Determine if the set of clusters and centers is satisfactory. If not, go to step 2 and repeat the
clustering process.
There are many different variations on what constitutes satisfactory ending conditions. The most ideal
stopping criteria are when the cluster assignments do not change any longer with successive iterations. If
there is no change in the centers, the solution perfectly minimizes the Euclidean distance sum for each
cluster, unique up to variations in ordering of the dimensions. In practice, determining the perfect clustering
of a data set is computationally intensive and may require an indefinite amount of time. Approximations of
perfect clustering are quicker to compute and usually produce sufficiently accurate results.
A useful termination condition for constructing approximate solutions is to place a tolerance on how much
the centers are moved in successive steps. If the total distance between the centers at subsequent steps of the
algorithm is less then a specific tolerance, the centers can be assumed to approximate the ideal solution.
Another potential termination condition is to limit the maximum number of steps that are executed. This
condition does not necessarily produce a usable approximation, but it does provide a way to halt execution.
This is required because there is no way to determine if the algorithm can terminate successfully for a given
data set.
Feature clustering is a very common data reduction method in use by clustering based spike sorting
software. A waveform segment is reduced to a single data point by extracting numerical quantities known
as features. Each feature is a single real-valued number extracted from the data. Examples of features are:
maximum amplitude in waveform segment, minimum, time to maximum, time to minimum, peak to peak
distance, sum of all values, maximum slope of peak, and so on.
A commonly used feature clustering analysis starts with two features. The features are then calculated for
each waveform segment and presented on a scatter plot, allowing the user to visually determine how many
clusters may be present. A k-means clustering analysis is then run on these two dimensional data points to
determine the center of the clusters in feature space. With the center known, each waveform segment is then
assigned to a cluster depending on the values of its features.
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Part C Analysis Functions 319
Clustering Settings

Number of clusters
After features have been extracted from the data, the data points constructed from the feature will be split
up into a number of groups. The number of clustering groups must be provided. Clustering will always
partition the data into this number of clusters. The output of a clustering analysis should be verified visually
and numerically to determine if the number of clusters matches the data.
Locate Centers
Clustering has a good potential to form the basis for classifiers to score physiological data. The clustering
implementation will allow for automatic learning of cluster center positions through expectation
maximization or for manually specified cluster center positions.
Manually
The manual method allows the centers of each cluster to be manually typed in and edited. Instead of
running a full k-means algorithm to locate centers, the k-means algorithm will simply run through the data
set and assign each element to the closest cluster center and apply any outlier detection.
This simplistic clustering will allow centers as computed from a previous run to be used in subsequent
clustering. Using manually specified centers is necessary to provide consistency when clustering data that
may occur in different experiments or different graph files. The use of manual centers allows for the
clustering implementation to be used as a classifier to compare new data sets to clusters as determined from
either ideal or previously scored data sets.
By Learning
The learning method will use the full k-means clustering algorithm as described above. This consists of
choosing candidate centers, computing mean distances, adjusting the candidate center positions, and
repeating until termination conditions are met.
The data set used to compute the center positions can either be the full data set or a subset of the data.
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320 AcqKnowledge 4 Software Guide
Training Set Definition
The training set is the set of data that is used during the iterative portion of the clustering algorithm that
learns the po